Starting phenix.real_space_refine on Thu Feb 5 17:43:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qws_53426/02_2026/9qws_53426.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qws_53426/02_2026/9qws_53426.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 { model { file = "/net/cci-nas-00/data/ceres_data/9qws_53426/02_2026/9qws_53426.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qws_53426/02_2026/9qws_53426.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qws_53426/02_2026/9qws_53426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qws_53426/02_2026/9qws_53426.map" } 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 118 5.16 5 C 11780 2.51 5 N 3218 2.21 5 O 3456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 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: 18574 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 762 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 288 Unresolved non-hydrogen angles: 360 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 15, 'PHE:plan': 4, 'ASP:plan': 9, 'ARG:plan': 6, 'ASN:plan1': 3, 'TYR:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 181 Chain: "A" Number of atoms: 8197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 8197 Classifications: {'peptide': 1036} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 34, 'TRANS': 1001} Chain breaks: 6 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 39} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 8197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 8197 Classifications: {'peptide': 1036} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 34, 'TRANS': 1001} Chain breaks: 6 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 39} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 762 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 288 Unresolved non-hydrogen angles: 360 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 15, 'PHE:plan': 4, 'ASP:plan': 9, 'ARG:plan': 6, 'ASN:plan1': 3, 'TYR:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 181 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 2871 SG CYS A3532 49.162 68.275 63.504 1.00 88.07 S ATOM 2892 SG CYS A3535 51.674 70.979 62.485 1.00 57.53 S ATOM 5025 SG CYS A3872 52.460 68.606 65.371 1.00 60.94 S ATOM 5047 SG CYS A3875 49.659 71.243 65.688 1.00 60.84 S ATOM 11395 SG CYS B3532 105.525 83.922 63.528 1.00 89.83 S ATOM 11416 SG CYS B3535 103.056 81.192 62.496 1.00 62.08 S ATOM 13549 SG CYS B3872 102.217 83.553 65.376 1.00 58.97 S ATOM 13571 SG CYS B3875 105.015 80.937 65.732 1.00 58.64 S Time building chain proxies: 4.12, per 1000 atoms: 0.22 Number of scatterers: 18574 At special positions: 0 Unit cell: (157.232, 153.428, 136.944, 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 118 16.00 O 3456 8.00 N 3218 7.00 C 11780 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: 1.42 Conformation dependent library (CDL) restraints added in 811.4 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 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4640 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 8 sheets defined 72.3% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'E' and resid 9 through 21 removed outlier: 3.642A pdb=" N PHE E 13 " --> pdb=" O GLN E 9 " (cutoff:3.500A) 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 39 removed outlier: 3.586A pdb=" N VAL E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET E 37 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 65 through 75 Processing helix chain 'E' and resid 83 through 94 Processing helix chain 'E' and resid 102 through 114 Processing helix chain 'E' and resid 118 through 129 Processing helix chain 'E' and resid 138 through 148 Processing helix chain 'A' and resid 3223 through 3247 removed outlier: 3.827A pdb=" N GLN A3247 " --> pdb=" O LEU A3243 " (cutoff:3.500A) Processing helix chain 'A' and resid 3265 through 3286 removed outlier: 3.845A pdb=" N HIS A3275 " --> pdb=" O SER A3271 " (cutoff:3.500A) Processing helix chain 'A' and resid 3286 through 3297 removed outlier: 3.752A 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 removed outlier: 3.560A pdb=" N LEU A3319 " --> pdb=" O VAL A3315 " (cutoff:3.500A) Processing helix chain 'A' and resid 3329 through 3338 removed outlier: 3.700A pdb=" N LEU A3333 " --> pdb=" O GLY A3329 " (cutoff:3.500A) Processing helix chain 'A' and resid 3387 through 3403 Processing helix chain 'A' and resid 3404 through 3417 removed outlier: 3.524A pdb=" N LEU A3417 " --> pdb=" O ARG A3413 " (cutoff:3.500A) Processing helix chain 'A' and resid 3421 through 3438 removed outlier: 3.644A pdb=" N ARG A3425 " --> pdb=" O SER A3421 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN A3438 " --> pdb=" O HIS A3434 " (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: 3.829A pdb=" N GLY A3462 " --> pdb=" O PRO A3459 " (cutoff:3.500A) removed outlier: 7.507A 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: 4.283A 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 3601 through 3606 removed outlier: 3.624A pdb=" N LEU A3605 " --> pdb=" O ALA A3601 " (cutoff:3.500A) Processing helix chain 'A' and resid 3728 through 3755 Processing helix chain 'A' and resid 3756 through 3770 removed outlier: 3.649A pdb=" N GLU A3769 " --> pdb=" O CYS A3765 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA A3770 " --> pdb=" O LYS A3766 " (cutoff:3.500A) Processing helix chain 'A' and resid 3793 through 3806 removed outlier: 3.580A pdb=" N ASP A3806 " --> pdb=" O GLU A3802 " (cutoff:3.500A) Processing helix chain 'A' and resid 3806 through 3842 removed outlier: 3.661A pdb=" N SER A3842 " --> pdb=" O ALA A3838 " (cutoff:3.500A) Processing helix chain 'A' and resid 3853 through 3860 Processing helix chain 'A' and resid 3861 through 3864 removed outlier: 3.664A 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: 3.761A pdb=" N GLU A3908 " --> pdb=" O GLY A3904 " (cutoff:3.500A) Processing helix chain 'A' and resid 3918 through 3933 removed outlier: 3.748A pdb=" N THR A3933 " --> pdb=" O MET A3929 " (cutoff:3.500A) Processing helix chain 'A' and resid 3936 through 3957 removed outlier: 3.776A pdb=" N GLY A3957 " --> pdb=" O THR A3953 " (cutoff:3.500A) Processing helix chain 'A' and resid 3961 through 3967 removed outlier: 4.134A pdb=" N ALA A3965 " --> pdb=" O ASN A3961 " (cutoff:3.500A) Processing helix chain 'A' and resid 3968 through 3981 removed outlier: 3.590A pdb=" N LYS A3981 " --> pdb=" O ASP A3977 " (cutoff:3.500A) Processing helix chain 'A' and resid 3985 through 4000 removed outlier: 3.624A 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 4032 through 4036 removed outlier: 3.665A pdb=" N LYS A4035 " --> pdb=" O LYS A4032 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP A4036 " --> pdb=" O LYS A4033 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4032 through 4036' 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: 3.503A pdb=" N CYS A4074 " --> pdb=" O ALA A4070 " (cutoff:3.500A) Processing helix chain 'A' and resid 4089 through 4113 Processing helix chain 'A' and resid 4128 through 4134 Processing helix chain 'A' and resid 4138 through 4152 removed outlier: 3.937A pdb=" N ARG A4142 " --> pdb=" O THR A4138 " (cutoff:3.500A) Processing helix chain 'A' and resid 4155 through 4169 removed outlier: 3.942A pdb=" N GLN A4161 " --> pdb=" O SER A4157 " (cutoff:3.500A) Processing helix chain 'A' and resid 4170 through 4174 removed outlier: 4.088A pdb=" N SER A4174 " --> pdb=" O ASP A4171 " (cutoff:3.500A) Processing helix chain 'A' and resid 4180 through 4191 removed outlier: 3.513A pdb=" N LYS A4189 " --> pdb=" O ALA A4185 " (cutoff:3.500A) Processing helix chain 'A' and resid 4193 through 4203 Processing helix chain 'A' and resid 4205 through 4227 Processing helix chain 'A' and resid 4235 through 4251 removed outlier: 4.656A 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 4258 through 4276 removed outlier: 3.521A pdb=" N LEU A4262 " --> pdb=" O PHE A4258 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N GLY A4264 " --> pdb=" O SER A4260 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N THR A4265 " --> pdb=" O ARG A4261 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A4276 " --> pdb=" O CYS A4272 " (cutoff:3.500A) Processing helix chain 'A' and resid 4281 through 4299 Processing helix chain 'A' and resid 4302 through 4320 removed outlier: 3.689A pdb=" N ARG A4319 " --> pdb=" O GLU A4315 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR A4320 " --> pdb=" O THR A4316 " (cutoff:3.500A) Processing helix chain 'A' and resid 4326 through 4339 Processing helix chain 'A' and resid 4477 through 4483 removed outlier: 3.519A pdb=" N GLN A4481 " --> pdb=" O GLY A4477 " (cutoff:3.500A) Processing helix chain 'A' and resid 4484 through 4494 Processing helix chain 'A' and resid 4501 through 4515 Processing helix chain 'C' and resid 292 through 296 Processing helix chain 'C' and resid 302 through 327 removed outlier: 3.673A pdb=" N THR C 327 " --> pdb=" O LEU C 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 3223 through 3247 removed outlier: 3.812A pdb=" N GLN B3247 " --> pdb=" O LEU B3243 " (cutoff:3.500A) Processing helix chain 'B' and resid 3265 through 3286 removed outlier: 3.824A pdb=" N HIS B3275 " --> pdb=" O SER B3271 " (cutoff:3.500A) Processing helix chain 'B' and resid 3286 through 3297 removed outlier: 3.755A 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 removed outlier: 3.561A pdb=" N LEU B3319 " --> pdb=" O VAL B3315 " (cutoff:3.500A) Processing helix chain 'B' and resid 3329 through 3338 removed outlier: 3.733A pdb=" N LEU B3333 " --> pdb=" O GLY B3329 " (cutoff:3.500A) Processing helix chain 'B' and resid 3387 through 3403 Processing helix chain 'B' and resid 3404 through 3417 removed outlier: 3.592A pdb=" N LEU B3417 " --> pdb=" O ARG B3413 " (cutoff:3.500A) Processing helix chain 'B' and resid 3421 through 3438 removed outlier: 3.651A pdb=" N ARG B3425 " --> pdb=" O SER B3421 " (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: 3.823A pdb=" N GLY B3462 " --> pdb=" O PRO B3459 " (cutoff:3.500A) removed outlier: 7.502A 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: 4.281A 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 3601 through 3606 removed outlier: 3.610A pdb=" N LEU B3605 " --> pdb=" O ALA B3601 " (cutoff:3.500A) Processing helix chain 'B' and resid 3728 through 3755 Processing helix chain 'B' and resid 3756 through 3770 removed outlier: 3.639A pdb=" N GLU B3769 " --> pdb=" O CYS B3765 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA B3770 " --> pdb=" O LYS B3766 " (cutoff:3.500A) Processing helix chain 'B' and resid 3793 through 3806 removed outlier: 3.595A pdb=" N ASP B3806 " --> pdb=" O GLU B3802 " (cutoff:3.500A) Processing helix chain 'B' and resid 3806 through 3842 removed outlier: 3.765A pdb=" N SER B3842 " --> pdb=" O ALA B3838 " (cutoff:3.500A) Processing helix chain 'B' and resid 3853 through 3860 Processing helix chain 'B' and resid 3861 through 3864 removed outlier: 3.718A 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 Processing helix chain 'B' and resid 3904 through 3912 removed outlier: 3.798A pdb=" N GLU B3908 " --> pdb=" O GLY B3904 " (cutoff:3.500A) Processing helix chain 'B' and resid 3918 through 3933 removed outlier: 3.763A pdb=" N THR B3933 " --> pdb=" O MET B3929 " (cutoff:3.500A) Processing helix chain 'B' and resid 3936 through 3957 removed outlier: 3.811A pdb=" N GLY B3957 " --> pdb=" O THR B3953 " (cutoff:3.500A) Processing helix chain 'B' and resid 3961 through 3967 removed outlier: 4.123A pdb=" N ALA B3965 " --> pdb=" O ASN B3961 " (cutoff:3.500A) Processing helix chain 'B' and resid 3968 through 3981 removed outlier: 3.582A pdb=" N LYS B3981 " --> pdb=" O ASP B3977 " (cutoff:3.500A) Processing helix chain 'B' and resid 3985 through 4000 removed outlier: 3.611A 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 4032 through 4036 removed outlier: 3.899A pdb=" N LYS B4035 " --> pdb=" O LYS B4032 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP B4036 " --> pdb=" O LYS B4033 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4032 through 4036' Processing helix chain 'B' and resid 4038 through 4042 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 removed outlier: 3.521A pdb=" N CYS B4074 " --> pdb=" O ALA B4070 " (cutoff:3.500A) Processing helix chain 'B' and resid 4089 through 4113 Processing helix chain 'B' and resid 4128 through 4134 Processing helix chain 'B' and resid 4138 through 4152 removed outlier: 3.919A pdb=" N ARG B4142 " --> pdb=" O THR B4138 " (cutoff:3.500A) Processing helix chain 'B' and resid 4155 through 4169 removed outlier: 3.949A pdb=" N GLN B4161 " --> pdb=" O SER B4157 " (cutoff:3.500A) Processing helix chain 'B' and resid 4170 through 4174 removed outlier: 4.033A pdb=" N SER B4174 " --> pdb=" O ASP B4171 " (cutoff:3.500A) Processing helix chain 'B' and resid 4180 through 4191 Processing helix chain 'B' and resid 4193 through 4203 Processing helix chain 'B' and resid 4205 through 4227 Processing helix chain 'B' and resid 4235 through 4251 removed outlier: 4.733A 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: 5.702A pdb=" N GLY B4264 " --> pdb=" O SER B4260 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N THR B4265 " --> pdb=" O ARG B4261 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B4276 " --> pdb=" O CYS B4272 " (cutoff:3.500A) Processing helix chain 'B' and resid 4281 through 4299 Processing helix chain 'B' and resid 4302 through 4320 removed outlier: 3.692A pdb=" N ARG B4319 " --> pdb=" O GLU B4315 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR B4320 " --> pdb=" O THR B4316 " (cutoff:3.500A) Processing helix chain 'B' and resid 4326 through 4339 Processing helix chain 'B' and resid 4477 through 4483 removed outlier: 3.591A pdb=" N GLN B4481 " --> pdb=" O GLY B4477 " (cutoff:3.500A) Processing helix chain 'B' and resid 4484 through 4494 Processing helix chain 'B' and resid 4501 through 4515 Processing helix chain 'D' and resid 292 through 296 Processing helix chain 'D' and resid 302 through 327 removed outlier: 3.727A pdb=" N THR D 327 " --> pdb=" O LEU D 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 21 Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 32 through 39 removed outlier: 3.575A pdb=" N VAL F 36 " --> pdb=" O GLU F 32 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET F 37 " --> pdb=" O LEU F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 57 Processing helix chain 'F' and resid 65 through 75 removed outlier: 3.525A pdb=" N ARG F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 Processing helix chain 'F' and resid 102 through 114 Processing helix chain 'F' and resid 118 through 129 Processing helix chain 'F' and resid 138 through 148 Processing sheet with id=AA1, first strand: chain 'A' and resid 3249 through 3251 Processing sheet with id=AA2, first strand: chain 'A' and resid 3543 through 3546 removed outlier: 3.831A pdb=" N LYS A3573 " --> pdb=" O TYR A3716 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLN A3560 " --> pdb=" O TYR A3556 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N TYR A3556 " --> pdb=" O GLN A3560 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL A3562 " --> pdb=" O THR A3554 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THR A3554 " --> pdb=" O VAL A3562 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS A3564 " --> pdb=" O VAL A3552 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 3543 through 3546 removed outlier: 3.831A pdb=" N LYS A3573 " --> pdb=" O TYR A3716 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N SER A3638 " --> pdb=" O LEU A3565 " (cutoff:3.500A) removed outlier: 10.947A pdb=" N GLY A3567 " --> pdb=" O VAL A3636 " (cutoff:3.500A) removed outlier: 9.680A pdb=" N VAL A3636 " --> pdb=" O GLY A3567 " (cutoff:3.500A) removed outlier: 9.979A pdb=" N HIS A3569 " --> pdb=" O PRO A3634 " (cutoff:3.500A) removed outlier: 10.546A pdb=" N ILE A3571 " --> pdb=" O PRO A3632 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LYS A3573 " --> pdb=" O ASP A3630 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASP A3630 " --> pdb=" O LYS A3573 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR A3575 " --> pdb=" O LYS A3628 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LYS A3628 " --> pdb=" O THR A3575 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS A3577 " --> pdb=" O GLU A3626 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU A3626 " --> pdb=" O LYS A3577 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N THR A3589 " --> pdb=" O ALA A3645 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS A3616 " --> pdb=" O LEU A3592 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N TYR A3594 " --> pdb=" O LYS A3614 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LYS A3614 " --> pdb=" O TYR A3594 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 4051 through 4052 Processing sheet with id=AA5, first strand: chain 'B' and resid 3249 through 3251 Processing sheet with id=AA6, first strand: chain 'B' and resid 3543 through 3546 removed outlier: 3.847A pdb=" N LYS B3573 " --> pdb=" O TYR B3716 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP B3553 " --> pdb=" O LYS B3564 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ILE B3566 " --> pdb=" O LYS B3551 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N LYS B3551 " --> pdb=" O ILE B3566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 3543 through 3546 removed outlier: 3.847A pdb=" N LYS B3573 " --> pdb=" O TYR B3716 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N SER B3638 " --> pdb=" O LEU B3565 " (cutoff:3.500A) removed outlier: 10.956A pdb=" N GLY B3567 " --> pdb=" O VAL B3636 " (cutoff:3.500A) removed outlier: 9.668A pdb=" N VAL B3636 " --> pdb=" O GLY B3567 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N HIS B3569 " --> pdb=" O PRO B3634 " (cutoff:3.500A) removed outlier: 10.605A pdb=" N ILE B3571 " --> pdb=" O PRO B3632 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LYS B3573 " --> pdb=" O ASP B3630 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP B3630 " --> pdb=" O LYS B3573 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR B3575 " --> pdb=" O LYS B3628 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LYS B3628 " --> pdb=" O THR B3575 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LYS B3577 " --> pdb=" O GLU B3626 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU B3626 " --> pdb=" O LYS B3577 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR B3589 " --> pdb=" O ALA B3645 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS B3616 " --> pdb=" O LEU B3592 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N TYR B3594 " --> pdb=" O LYS B3614 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LYS B3614 " --> pdb=" O TYR B3594 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 4051 through 4052 1236 hydrogen bonds defined for protein. 3630 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: 3.25 Time building geometry restraints manager: 1.86 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: 6107 1.34 - 1.46: 3977 1.46 - 1.58: 8614 1.58 - 1.70: 0 1.70 - 1.82: 164 Bond restraints: 18862 Sorted by residual: bond pdb=" CB TRP A3959 " pdb=" CG TRP A3959 " ideal model delta sigma weight residual 1.498 1.460 0.038 3.10e-02 1.04e+03 1.48e+00 bond pdb=" CB GLU A4252 " pdb=" CG GLU A4252 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.40e+00 bond pdb=" CA ASN B3701 " pdb=" CB ASN B3701 " ideal model delta sigma weight residual 1.528 1.548 -0.019 1.66e-02 3.63e+03 1.36e+00 bond pdb=" CB ASN B4126 " pdb=" CG ASN B4126 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.24e+00 bond pdb=" CB GLU B3730 " pdb=" CG GLU B3730 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.20e+00 ... (remaining 18857 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 25396 2.77 - 5.54: 128 5.54 - 8.31: 9 8.31 - 11.08: 1 11.08 - 13.85: 2 Bond angle restraints: 25536 Sorted by residual: angle pdb=" CA LEU B4097 " pdb=" CB LEU B4097 " pdb=" CG LEU B4097 " ideal model delta sigma weight residual 116.30 130.15 -13.85 3.50e+00 8.16e-02 1.57e+01 angle pdb=" N ILE E 131 " pdb=" CA ILE E 131 " pdb=" C ILE E 131 " ideal model delta sigma weight residual 113.42 108.84 4.58 1.17e+00 7.31e-01 1.53e+01 angle pdb=" C ASN B4126 " pdb=" CA ASN B4126 " pdb=" CB ASN B4126 " ideal model delta sigma weight residual 109.70 116.52 -6.82 1.81e+00 3.05e-01 1.42e+01 angle pdb=" CA LEU A4097 " pdb=" CB LEU A4097 " pdb=" CG LEU A4097 " ideal model delta sigma weight residual 116.30 129.17 -12.87 3.50e+00 8.16e-02 1.35e+01 angle pdb=" CA ASN B4126 " pdb=" CB ASN B4126 " pdb=" CG ASN B4126 " ideal model delta sigma weight residual 112.60 115.78 -3.18 1.00e+00 1.00e+00 1.01e+01 ... (remaining 25531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.07: 9990 18.07 - 36.15: 1236 36.15 - 54.22: 248 54.22 - 72.30: 32 72.30 - 90.37: 24 Dihedral angle restraints: 11530 sinusoidal: 4424 harmonic: 7106 Sorted by residual: dihedral pdb=" CA LYS A3608 " pdb=" C LYS A3608 " pdb=" N PRO A3609 " pdb=" CA PRO A3609 " ideal model delta harmonic sigma weight residual -180.00 -159.48 -20.52 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA LYS B3608 " pdb=" C LYS B3608 " pdb=" N PRO B3609 " pdb=" CA PRO B3609 " ideal model delta harmonic sigma weight residual -180.00 -160.15 -19.85 0 5.00e+00 4.00e-02 1.58e+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 -160.74 -19.26 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 11527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2115 0.034 - 0.068: 705 0.068 - 0.102: 130 0.102 - 0.136: 71 0.136 - 0.170: 5 Chirality restraints: 3026 Sorted by residual: chirality pdb=" CG LEU A3227 " pdb=" CB LEU A3227 " pdb=" CD1 LEU A3227 " pdb=" CD2 LEU A3227 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.26e-01 chirality pdb=" CG LEU A4228 " pdb=" CB LEU A4228 " pdb=" CD1 LEU A4228 " pdb=" CD2 LEU A4228 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" CA PRO A3609 " pdb=" N PRO A3609 " pdb=" C PRO A3609 " pdb=" CB PRO A3609 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.34e-01 ... (remaining 3023 not shown) Planarity restraints: 3230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B4155 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO B4156 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B4156 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B4156 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU B3388 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.15e+00 pdb=" CD GLU B3388 " 0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU B3388 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU B3388 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A4155 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO A4156 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A4156 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A4156 " -0.024 5.00e-02 4.00e+02 ... (remaining 3227 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 7114 2.91 - 3.40: 18667 3.40 - 3.90: 30208 3.90 - 4.40: 32269 4.40 - 4.90: 54991 Nonbonded interactions: 143249 Sorted by model distance: nonbonded pdb=" O ASN B4126 " pdb=" OD1 ASN B4126 " model vdw 2.408 3.040 nonbonded pdb=" O SER D 311 " pdb=" OD1 ASP D 315 " model vdw 2.421 3.040 nonbonded pdb=" O SER C 311 " pdb=" OD1 ASP C 315 " model vdw 2.424 3.040 nonbonded pdb=" O ASN F 43 " pdb=" ND2 ASN F 43 " model vdw 2.448 3.120 nonbonded pdb=" N GLU A4252 " pdb=" OE1 GLU A4252 " model vdw 2.527 3.120 ... (remaining 143244 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 3.930 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: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.000 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 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 : 0.003 0.038 18870 Z= 0.150 Angle : 0.555 13.849 25548 Z= 0.295 Chirality : 0.037 0.170 3026 Planarity : 0.004 0.045 3230 Dihedral : 16.376 90.373 6890 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.69 % Allowed : 16.82 % Favored : 81.49 % 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: 2.08 (0.18), residues: 2366 helix: 2.20 (0.13), residues: 1584 sheet: 0.54 (0.56), residues: 98 loop : -0.45 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 330 TYR 0.014 0.001 TYR B3912 PHE 0.016 0.001 PHE A4498 TRP 0.027 0.002 TRP A4103 HIS 0.006 0.001 HIS A3429 Details of bonding type rmsd covalent geometry : bond 0.00347 (18862) covalent geometry : angle 0.55394 (25536) hydrogen bonds : bond 0.12971 ( 1214) hydrogen bonds : angle 4.69955 ( 3630) metal coordination : bond 0.00196 ( 8) metal coordination : angle 1.56775 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 235 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: E 30 THR cc_start: 0.6231 (p) cc_final: 0.5924 (p) REVERT: E 50 GLN cc_start: 0.5329 (mm-40) cc_final: 0.5126 (mm-40) REVERT: A 3554 THR cc_start: 0.6927 (OUTLIER) cc_final: 0.6339 (m) REVERT: A 3832 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.8162 (t0) REVERT: A 4290 MET cc_start: 0.8541 (mtp) cc_final: 0.8320 (mtm) REVERT: B 3231 HIS cc_start: 0.7888 (t70) cc_final: 0.7560 (t70) REVERT: B 3555 ARG cc_start: 0.7163 (ttt-90) cc_final: 0.6952 (ttt-90) REVERT: B 3588 ARG cc_start: 0.3622 (mmt-90) cc_final: 0.3322 (mmt-90) REVERT: B 3614 LYS cc_start: 0.8408 (tptm) cc_final: 0.8034 (mmmt) REVERT: B 3832 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.7977 (t0) REVERT: B 4035 LYS cc_start: 0.7530 (mmmt) cc_final: 0.7326 (mmmt) REVERT: F 19 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7615 (tt) REVERT: F 30 THR cc_start: 0.6232 (p) cc_final: 0.5898 (p) REVERT: F 66 PHE cc_start: 0.6139 (t80) cc_final: 0.5797 (t80) outliers start: 33 outliers final: 25 residues processed: 260 average time/residue: 0.1554 time to fit residues: 60.8272 Evaluate side-chains 258 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 229 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain A residue 3230 LEU Chi-restraints excluded: chain A residue 3244 LEU Chi-restraints excluded: chain A residue 3311 VAL Chi-restraints excluded: chain A residue 3315 VAL Chi-restraints excluded: chain A residue 3550 ILE Chi-restraints excluded: chain A residue 3554 THR Chi-restraints excluded: chain A residue 3625 THR Chi-restraints excluded: chain A residue 3724 ASP Chi-restraints excluded: chain A residue 3832 ASP Chi-restraints excluded: chain A residue 4126 ASN Chi-restraints excluded: chain A residue 4184 LEU Chi-restraints excluded: chain A residue 4230 THR Chi-restraints excluded: chain A residue 4277 VAL Chi-restraints excluded: chain B residue 3230 LEU Chi-restraints excluded: chain B residue 3244 LEU Chi-restraints excluded: chain B residue 3311 VAL Chi-restraints excluded: chain B residue 3540 VAL Chi-restraints excluded: chain B residue 3550 ILE Chi-restraints excluded: chain B residue 3566 ILE Chi-restraints excluded: chain B residue 3627 VAL Chi-restraints excluded: chain B residue 3724 ASP Chi-restraints excluded: chain B residue 3832 ASP Chi-restraints excluded: chain B residue 3968 LEU Chi-restraints excluded: chain B residue 4077 ILE Chi-restraints excluded: chain B residue 4223 LEU Chi-restraints excluded: chain B residue 4229 SER Chi-restraints excluded: chain B residue 4277 VAL Chi-restraints excluded: chain F residue 19 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 9.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 43 ASN E 54 ASN A3738 ASN A4050 ASN B3738 ASN B4126 ASN B4234 GLN F 43 ASN F 50 GLN F 54 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.151336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.107039 restraints weight = 26450.596| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.41 r_work: 0.3099 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18870 Z= 0.168 Angle : 0.517 8.962 25548 Z= 0.267 Chirality : 0.038 0.145 3026 Planarity : 0.004 0.043 3230 Dihedral : 5.119 52.738 2634 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.17 % Allowed : 16.05 % Favored : 80.78 % 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: 2.29 (0.17), residues: 2366 helix: 2.34 (0.13), residues: 1588 sheet: 0.89 (0.56), residues: 94 loop : -0.37 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B3252 TYR 0.012 0.002 TYR A3856 PHE 0.011 0.001 PHE A3293 TRP 0.012 0.001 TRP A4103 HIS 0.008 0.001 HIS B3429 Details of bonding type rmsd covalent geometry : bond 0.00408 (18862) covalent geometry : angle 0.51634 (25536) hydrogen bonds : bond 0.04755 ( 1214) hydrogen bonds : angle 3.52996 ( 3630) metal coordination : bond 0.00184 ( 8) metal coordination : angle 1.52364 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 231 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: E 30 THR cc_start: 0.6859 (p) cc_final: 0.6583 (p) REVERT: E 32 GLU cc_start: 0.5921 (mp0) cc_final: 0.5594 (mp0) REVERT: E 46 GLU cc_start: 0.6426 (tt0) cc_final: 0.5727 (tp30) REVERT: E 57 ASP cc_start: 0.4625 (t0) cc_final: 0.4365 (t0) REVERT: A 3272 LEU cc_start: 0.8874 (tp) cc_final: 0.8562 (tp) REVERT: A 3310 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8978 (mt) REVERT: A 3554 THR cc_start: 0.7340 (OUTLIER) cc_final: 0.6769 (m) REVERT: A 4290 MET cc_start: 0.8564 (mtp) cc_final: 0.8355 (mtm) REVERT: A 4502 ARG cc_start: 0.6092 (ptt-90) cc_final: 0.5335 (ttp80) REVERT: C 330 ARG cc_start: 0.6885 (ptp-110) cc_final: 0.6609 (ttm110) REVERT: B 3231 HIS cc_start: 0.7977 (t70) cc_final: 0.7671 (t70) REVERT: B 3310 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8989 (mt) REVERT: B 3614 LYS cc_start: 0.8424 (tptm) cc_final: 0.7962 (mmmt) REVERT: B 3959 TRP cc_start: 0.6513 (OUTLIER) cc_final: 0.6172 (t60) REVERT: B 3963 ASP cc_start: 0.5820 (OUTLIER) cc_final: 0.5306 (t0) REVERT: B 4126 ASN cc_start: 0.7051 (OUTLIER) cc_final: 0.6748 (p0) REVERT: B 4223 LEU cc_start: 0.8254 (tt) cc_final: 0.7997 (tp) REVERT: B 4498 PHE cc_start: 0.4830 (t80) cc_final: 0.4514 (t80) REVERT: F 30 THR cc_start: 0.6784 (p) cc_final: 0.6512 (p) REVERT: F 32 GLU cc_start: 0.6344 (mp0) cc_final: 0.5741 (mp0) REVERT: F 46 GLU cc_start: 0.7258 (tp30) cc_final: 0.7002 (tp30) REVERT: F 66 PHE cc_start: 0.6782 (t80) cc_final: 0.6511 (t80) outliers start: 62 outliers final: 34 residues processed: 272 average time/residue: 0.1489 time to fit residues: 62.2637 Evaluate side-chains 264 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 224 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain A residue 3244 LEU Chi-restraints excluded: chain A residue 3282 ILE Chi-restraints excluded: chain A residue 3310 LEU Chi-restraints excluded: chain A residue 3311 VAL Chi-restraints excluded: chain A residue 3315 VAL Chi-restraints excluded: chain A residue 3409 ILE Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3554 THR Chi-restraints excluded: chain A residue 3566 ILE Chi-restraints excluded: chain A residue 3605 LEU Chi-restraints excluded: chain A residue 3627 VAL Chi-restraints excluded: chain A residue 3792 VAL Chi-restraints excluded: chain A residue 3867 THR Chi-restraints excluded: chain A residue 3869 SER Chi-restraints excluded: chain A residue 3963 ASP Chi-restraints excluded: chain A residue 4230 THR Chi-restraints excluded: chain A residue 4263 VAL Chi-restraints excluded: chain A residue 4327 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain B residue 3244 LEU Chi-restraints excluded: chain B residue 3282 ILE Chi-restraints excluded: chain B residue 3310 LEU Chi-restraints excluded: chain B residue 3311 VAL Chi-restraints excluded: chain B residue 3409 ILE Chi-restraints excluded: chain B residue 3566 ILE Chi-restraints excluded: chain B residue 3627 VAL Chi-restraints excluded: chain B residue 3867 THR Chi-restraints excluded: chain B residue 3869 SER Chi-restraints excluded: chain B residue 3959 TRP Chi-restraints excluded: chain B residue 3963 ASP Chi-restraints excluded: chain B residue 3968 LEU Chi-restraints excluded: chain B residue 4051 GLU Chi-restraints excluded: chain B residue 4077 ILE Chi-restraints excluded: chain B residue 4126 ASN Chi-restraints excluded: chain B residue 4327 THR Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain F residue 19 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 115 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 211 optimal weight: 0.1980 chunk 187 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 235 optimal weight: 9.9990 chunk 205 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3738 ASN B3738 ASN B4257 HIS F 43 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.153979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.108576 restraints weight = 26727.084| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.30 r_work: 0.3143 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18870 Z= 0.104 Angle : 0.451 11.314 25548 Z= 0.234 Chirality : 0.036 0.143 3026 Planarity : 0.003 0.041 3230 Dihedral : 4.165 45.996 2607 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.22 % Allowed : 16.36 % Favored : 80.42 % 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: 2.67 (0.18), residues: 2366 helix: 2.68 (0.13), residues: 1582 sheet: 1.23 (0.58), residues: 94 loop : -0.39 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3252 TYR 0.011 0.001 TYR B4101 PHE 0.010 0.001 PHE A3293 TRP 0.013 0.001 TRP A4103 HIS 0.006 0.001 HIS A3429 Details of bonding type rmsd covalent geometry : bond 0.00235 (18862) covalent geometry : angle 0.45121 (25536) hydrogen bonds : bond 0.03709 ( 1214) hydrogen bonds : angle 3.22307 ( 3630) metal coordination : bond 0.00151 ( 8) metal coordination : angle 0.79585 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 246 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: E 19 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.7106 (tp) REVERT: E 30 THR cc_start: 0.6803 (p) cc_final: 0.6545 (p) REVERT: E 32 GLU cc_start: 0.5878 (mp0) cc_final: 0.5557 (mp0) REVERT: E 46 GLU cc_start: 0.6408 (tt0) cc_final: 0.5747 (tp30) REVERT: A 3227 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7136 (tp) REVERT: A 3247 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.7374 (mp10) REVERT: A 3272 LEU cc_start: 0.8753 (tp) cc_final: 0.8412 (tp) REVERT: A 4229 SER cc_start: 0.8493 (OUTLIER) cc_final: 0.8007 (t) REVERT: A 4290 MET cc_start: 0.8493 (mtp) cc_final: 0.8285 (mtm) REVERT: A 4502 ARG cc_start: 0.6119 (ptt-90) cc_final: 0.5290 (ttp80) REVERT: C 330 ARG cc_start: 0.6808 (ptp-110) cc_final: 0.6591 (ttm110) REVERT: B 3231 HIS cc_start: 0.7936 (t70) cc_final: 0.7663 (t70) REVERT: B 3247 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.7341 (mp10) REVERT: B 3530 ASP cc_start: 0.7063 (t0) cc_final: 0.6853 (t0) REVERT: B 3546 LYS cc_start: 0.7654 (pttp) cc_final: 0.7106 (mttt) REVERT: B 3614 LYS cc_start: 0.8447 (tptm) cc_final: 0.7980 (mmmt) REVERT: B 3832 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.8046 (t0) REVERT: B 3959 TRP cc_start: 0.6407 (OUTLIER) cc_final: 0.6074 (t60) REVERT: B 4229 SER cc_start: 0.8392 (m) cc_final: 0.8108 (t) REVERT: B 4498 PHE cc_start: 0.4921 (t80) cc_final: 0.4493 (t80) REVERT: F 30 THR cc_start: 0.6695 (p) cc_final: 0.6453 (p) REVERT: F 32 GLU cc_start: 0.6215 (mp0) cc_final: 0.5674 (mp0) REVERT: F 46 GLU cc_start: 0.7295 (tp30) cc_final: 0.6874 (tp30) REVERT: F 50 GLN cc_start: 0.5880 (mm-40) cc_final: 0.5091 (mm-40) outliers start: 63 outliers final: 30 residues processed: 296 average time/residue: 0.1457 time to fit residues: 66.3152 Evaluate side-chains 264 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 227 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain A residue 3224 TYR Chi-restraints excluded: chain A residue 3227 LEU Chi-restraints excluded: chain A residue 3244 LEU Chi-restraints excluded: chain A residue 3247 GLN Chi-restraints excluded: chain A residue 3307 VAL Chi-restraints excluded: chain A residue 3311 VAL Chi-restraints excluded: chain A residue 3315 VAL Chi-restraints excluded: chain A residue 3409 ILE Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3581 LEU Chi-restraints excluded: chain A residue 3627 VAL Chi-restraints excluded: chain A residue 3959 TRP Chi-restraints excluded: chain A residue 4126 ASN Chi-restraints excluded: chain A residue 4193 SER Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4228 LEU Chi-restraints excluded: chain A residue 4229 SER Chi-restraints excluded: chain A residue 4230 THR Chi-restraints excluded: chain A residue 4327 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain B residue 3244 LEU Chi-restraints excluded: chain B residue 3247 GLN Chi-restraints excluded: chain B residue 3307 VAL Chi-restraints excluded: chain B residue 3311 VAL Chi-restraints excluded: chain B residue 3409 ILE Chi-restraints excluded: chain B residue 3581 LEU Chi-restraints excluded: chain B residue 3832 ASP Chi-restraints excluded: chain B residue 3959 TRP Chi-restraints excluded: chain B residue 3968 LEU Chi-restraints excluded: chain B residue 4327 THR Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain F residue 19 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 198 optimal weight: 0.0970 chunk 23 optimal weight: 0.9990 chunk 137 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 148 optimal weight: 8.9990 chunk 188 optimal weight: 1.9990 chunk 87 optimal weight: 0.2980 chunk 108 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 189 optimal weight: 0.7980 chunk 239 optimal weight: 20.0000 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3738 ASN B3738 ASN F 43 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.154984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.108390 restraints weight = 26562.527| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.08 r_work: 0.3167 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18870 Z= 0.092 Angle : 0.438 9.004 25548 Z= 0.225 Chirality : 0.035 0.143 3026 Planarity : 0.003 0.041 3230 Dihedral : 3.991 46.963 2601 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.48 % Allowed : 16.00 % Favored : 80.52 % 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: 2.94 (0.18), residues: 2366 helix: 2.89 (0.13), residues: 1582 sheet: 1.37 (0.59), residues: 94 loop : -0.29 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3252 TYR 0.013 0.001 TYR A3856 PHE 0.010 0.001 PHE B3293 TRP 0.015 0.001 TRP A4103 HIS 0.006 0.001 HIS B3429 Details of bonding type rmsd covalent geometry : bond 0.00203 (18862) covalent geometry : angle 0.43822 (25536) hydrogen bonds : bond 0.03315 ( 1214) hydrogen bonds : angle 3.04614 ( 3630) metal coordination : bond 0.00140 ( 8) metal coordination : angle 0.58125 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 237 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: E 19 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.7129 (tp) REVERT: E 30 THR cc_start: 0.6738 (p) cc_final: 0.6493 (p) REVERT: E 32 GLU cc_start: 0.6004 (mp0) cc_final: 0.5677 (mp0) REVERT: E 46 GLU cc_start: 0.6359 (tt0) cc_final: 0.5689 (tp30) REVERT: A 3227 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7171 (tp) REVERT: A 3247 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.7388 (mp10) REVERT: A 3272 LEU cc_start: 0.8945 (tp) cc_final: 0.8714 (tp) REVERT: A 3477 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8904 (mt) REVERT: A 3528 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: A 3612 TRP cc_start: 0.8527 (m100) cc_final: 0.8124 (m100) REVERT: A 3832 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.8030 (t0) REVERT: A 4332 PHE cc_start: 0.7483 (m-10) cc_final: 0.7257 (m-10) REVERT: A 4502 ARG cc_start: 0.6132 (ptt-90) cc_final: 0.5295 (ttp80) REVERT: C 330 ARG cc_start: 0.6800 (ptp-110) cc_final: 0.6567 (ttm110) REVERT: B 3231 HIS cc_start: 0.7912 (t70) cc_final: 0.7638 (t70) REVERT: B 3247 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.7369 (mp10) REVERT: B 3528 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: B 3530 ASP cc_start: 0.6990 (t0) cc_final: 0.6782 (t0) REVERT: B 3546 LYS cc_start: 0.7657 (pttp) cc_final: 0.7294 (mttp) REVERT: B 3614 LYS cc_start: 0.8463 (tptm) cc_final: 0.8021 (mmmt) REVERT: B 3832 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.8020 (t0) REVERT: B 3959 TRP cc_start: 0.6291 (OUTLIER) cc_final: 0.5993 (t60) REVERT: B 4229 SER cc_start: 0.8340 (m) cc_final: 0.8084 (t) REVERT: B 4498 PHE cc_start: 0.4860 (t80) cc_final: 0.4468 (t80) REVERT: F 32 GLU cc_start: 0.6218 (mp0) cc_final: 0.5706 (mp0) REVERT: F 46 GLU cc_start: 0.7361 (tp30) cc_final: 0.6902 (tp30) REVERT: F 50 GLN cc_start: 0.5949 (mm-40) cc_final: 0.4973 (mm-40) outliers start: 68 outliers final: 36 residues processed: 286 average time/residue: 0.1437 time to fit residues: 62.9647 Evaluate side-chains 265 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 219 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain A residue 3224 TYR Chi-restraints excluded: chain A residue 3227 LEU Chi-restraints excluded: chain A residue 3244 LEU Chi-restraints excluded: chain A residue 3247 GLN Chi-restraints excluded: chain A residue 3307 VAL Chi-restraints excluded: chain A residue 3311 VAL Chi-restraints excluded: chain A residue 3315 VAL Chi-restraints excluded: chain A residue 3409 ILE Chi-restraints excluded: chain A residue 3477 LEU Chi-restraints excluded: chain A residue 3528 GLU Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3566 ILE Chi-restraints excluded: chain A residue 3581 LEU Chi-restraints excluded: chain A residue 3627 VAL Chi-restraints excluded: chain A residue 3832 ASP Chi-restraints excluded: chain A residue 3959 TRP Chi-restraints excluded: chain A residue 3979 ILE Chi-restraints excluded: chain A residue 4024 ILE Chi-restraints excluded: chain A residue 4126 ASN Chi-restraints excluded: chain A residue 4193 SER Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4230 THR Chi-restraints excluded: chain A residue 4327 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain B residue 3244 LEU Chi-restraints excluded: chain B residue 3247 GLN Chi-restraints excluded: chain B residue 3307 VAL Chi-restraints excluded: chain B residue 3311 VAL Chi-restraints excluded: chain B residue 3409 ILE Chi-restraints excluded: chain B residue 3528 GLU Chi-restraints excluded: chain B residue 3581 LEU Chi-restraints excluded: chain B residue 3627 VAL Chi-restraints excluded: chain B residue 3761 GLU Chi-restraints excluded: chain B residue 3832 ASP Chi-restraints excluded: chain B residue 3959 TRP Chi-restraints excluded: chain B residue 3968 LEU Chi-restraints excluded: chain B residue 4024 ILE Chi-restraints excluded: chain B residue 4077 ILE Chi-restraints excluded: chain B residue 4277 VAL Chi-restraints excluded: chain B residue 4327 THR Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain F residue 19 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 120 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 15 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 208 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 43 ASN F 43 ASN 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 = 0.151560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.105770 restraints weight = 26559.198| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.27 r_work: 0.3106 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18870 Z= 0.156 Angle : 0.499 8.230 25548 Z= 0.254 Chirality : 0.037 0.136 3026 Planarity : 0.004 0.041 3230 Dihedral : 4.203 45.422 2601 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.58 % Allowed : 15.90 % Favored : 80.52 % 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: 2.66 (0.18), residues: 2366 helix: 2.63 (0.13), residues: 1598 sheet: 1.41 (0.58), residues: 94 loop : -0.39 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B3252 TYR 0.015 0.001 TYR B3856 PHE 0.009 0.001 PHE A3293 TRP 0.017 0.001 TRP B4103 HIS 0.007 0.001 HIS B3429 Details of bonding type rmsd covalent geometry : bond 0.00379 (18862) covalent geometry : angle 0.49729 (25536) hydrogen bonds : bond 0.04405 ( 1214) hydrogen bonds : angle 3.24068 ( 3630) metal coordination : bond 0.00232 ( 8) metal coordination : angle 1.79430 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 229 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: E 30 THR cc_start: 0.6841 (p) cc_final: 0.6601 (p) REVERT: E 32 GLU cc_start: 0.5989 (mp0) cc_final: 0.5649 (mp0) REVERT: E 46 GLU cc_start: 0.6886 (tt0) cc_final: 0.6262 (tp30) REVERT: A 3227 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7288 (tp) REVERT: A 3247 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.7355 (mp10) REVERT: A 3272 LEU cc_start: 0.8869 (tp) cc_final: 0.8642 (tp) REVERT: A 3528 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7353 (mp0) REVERT: A 4488 MET cc_start: 0.7113 (mtm) cc_final: 0.6811 (mtp) REVERT: A 4502 ARG cc_start: 0.6093 (ptt-90) cc_final: 0.5250 (ttp80) REVERT: C 330 ARG cc_start: 0.6782 (ptp-110) cc_final: 0.6536 (ttm110) REVERT: B 3231 HIS cc_start: 0.7982 (t70) cc_final: 0.7693 (t70) REVERT: B 3247 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.7377 (mp10) REVERT: B 3528 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: B 3546 LYS cc_start: 0.7619 (pttp) cc_final: 0.7155 (mttp) REVERT: B 3614 LYS cc_start: 0.8466 (tptm) cc_final: 0.7970 (mmmt) REVERT: B 3754 MET cc_start: 0.8589 (mmm) cc_final: 0.8271 (mmm) REVERT: B 3829 LEU cc_start: 0.9030 (tp) cc_final: 0.8786 (tt) REVERT: B 3959 TRP cc_start: 0.6481 (OUTLIER) cc_final: 0.6115 (t60) REVERT: B 4229 SER cc_start: 0.8410 (m) cc_final: 0.8174 (t) REVERT: B 4498 PHE cc_start: 0.4906 (t80) cc_final: 0.4557 (t80) REVERT: F 32 GLU cc_start: 0.6091 (mp0) cc_final: 0.5638 (mp0) REVERT: F 50 GLN cc_start: 0.6701 (mm-40) cc_final: 0.5953 (mm-40) outliers start: 70 outliers final: 51 residues processed: 275 average time/residue: 0.1442 time to fit residues: 61.3668 Evaluate side-chains 280 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 223 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain A residue 3227 LEU Chi-restraints excluded: chain A residue 3244 LEU Chi-restraints excluded: chain A residue 3247 GLN Chi-restraints excluded: chain A residue 3282 ILE Chi-restraints excluded: chain A residue 3307 VAL Chi-restraints excluded: chain A residue 3311 VAL Chi-restraints excluded: chain A residue 3315 VAL Chi-restraints excluded: chain A residue 3409 ILE Chi-restraints excluded: chain A residue 3528 GLU Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3566 ILE Chi-restraints excluded: chain A residue 3581 LEU Chi-restraints excluded: chain A residue 3605 LEU Chi-restraints excluded: chain A residue 3625 THR Chi-restraints excluded: chain A residue 3627 VAL Chi-restraints excluded: chain A residue 3747 ASP Chi-restraints excluded: chain A residue 3869 SER Chi-restraints excluded: chain A residue 3959 TRP Chi-restraints excluded: chain A residue 3963 ASP Chi-restraints excluded: chain A residue 3979 ILE Chi-restraints excluded: chain A residue 4024 ILE Chi-restraints excluded: chain A residue 4126 ASN Chi-restraints excluded: chain A residue 4193 SER Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4230 THR Chi-restraints excluded: chain A residue 4277 VAL Chi-restraints excluded: chain A residue 4327 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain B residue 3244 LEU Chi-restraints excluded: chain B residue 3247 GLN Chi-restraints excluded: chain B residue 3272 LEU Chi-restraints excluded: chain B residue 3282 ILE Chi-restraints excluded: chain B residue 3307 VAL Chi-restraints excluded: chain B residue 3311 VAL Chi-restraints excluded: chain B residue 3409 ILE Chi-restraints excluded: chain B residue 3528 GLU Chi-restraints excluded: chain B residue 3550 ILE Chi-restraints excluded: chain B residue 3566 ILE Chi-restraints excluded: chain B residue 3581 LEU Chi-restraints excluded: chain B residue 3605 LEU Chi-restraints excluded: chain B residue 3627 VAL Chi-restraints excluded: chain B residue 3869 SER Chi-restraints excluded: chain B residue 3959 TRP Chi-restraints excluded: chain B residue 3963 ASP Chi-restraints excluded: chain B residue 3968 LEU Chi-restraints excluded: chain B residue 3979 ILE Chi-restraints excluded: chain B residue 4024 ILE Chi-restraints excluded: chain B residue 4077 ILE Chi-restraints excluded: chain B residue 4223 LEU Chi-restraints excluded: chain B residue 4277 VAL Chi-restraints excluded: chain B residue 4327 THR Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 57 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 41 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 214 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 11 optimal weight: 20.0000 chunk 183 optimal weight: 0.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 43 ASN 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 = 0.152538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.107176 restraints weight = 26495.803| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.25 r_work: 0.3125 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18870 Z= 0.125 Angle : 0.466 9.761 25548 Z= 0.238 Chirality : 0.036 0.152 3026 Planarity : 0.003 0.041 3230 Dihedral : 4.156 55.885 2601 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.22 % Allowed : 16.36 % Favored : 80.42 % 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 (0.18), residues: 2366 helix: 2.72 (0.13), residues: 1602 sheet: 1.51 (0.58), residues: 94 loop : -0.39 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3252 TYR 0.013 0.001 TYR B4101 PHE 0.009 0.001 PHE A3293 TRP 0.019 0.001 TRP B4103 HIS 0.006 0.001 HIS A3429 Details of bonding type rmsd covalent geometry : bond 0.00298 (18862) covalent geometry : angle 0.46577 (25536) hydrogen bonds : bond 0.03891 ( 1214) hydrogen bonds : angle 3.12395 ( 3630) metal coordination : bond 0.00126 ( 8) metal coordination : angle 0.90169 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 232 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: E 30 THR cc_start: 0.6855 (p) cc_final: 0.6602 (p) REVERT: E 32 GLU cc_start: 0.6006 (mp0) cc_final: 0.5417 (mp0) REVERT: E 46 GLU cc_start: 0.6518 (tt0) cc_final: 0.5883 (tp30) REVERT: A 3247 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.7326 (mp10) REVERT: A 3528 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: A 3554 THR cc_start: 0.7226 (OUTLIER) cc_final: 0.6777 (m) REVERT: A 3832 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.8018 (t0) REVERT: A 4488 MET cc_start: 0.7038 (mtm) cc_final: 0.6681 (mtp) REVERT: A 4502 ARG cc_start: 0.6068 (ptt-90) cc_final: 0.5260 (ttp80) REVERT: C 330 ARG cc_start: 0.6777 (ptp-110) cc_final: 0.6516 (ttm110) REVERT: B 3231 HIS cc_start: 0.7975 (t70) cc_final: 0.7702 (t70) REVERT: B 3247 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.7302 (mp10) REVERT: B 3528 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7294 (mp0) REVERT: B 3530 ASP cc_start: 0.7231 (t0) cc_final: 0.7021 (t0) REVERT: B 3546 LYS cc_start: 0.7612 (pttp) cc_final: 0.7193 (mttt) REVERT: B 3614 LYS cc_start: 0.8473 (tptm) cc_final: 0.7973 (mmmt) REVERT: B 3829 LEU cc_start: 0.9014 (tp) cc_final: 0.8748 (tt) REVERT: B 3832 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.8038 (t0) REVERT: B 3959 TRP cc_start: 0.6403 (OUTLIER) cc_final: 0.6067 (t60) REVERT: B 3963 ASP cc_start: 0.5600 (OUTLIER) cc_final: 0.5344 (t0) REVERT: B 4229 SER cc_start: 0.8425 (m) cc_final: 0.8146 (t) REVERT: B 4498 PHE cc_start: 0.4843 (t80) cc_final: 0.4480 (t80) REVERT: F 32 GLU cc_start: 0.6217 (mp0) cc_final: 0.5704 (mp0) REVERT: F 46 GLU cc_start: 0.7619 (tp30) cc_final: 0.7319 (tp30) REVERT: F 50 GLN cc_start: 0.6661 (mm-40) cc_final: 0.5829 (mm-40) outliers start: 63 outliers final: 44 residues processed: 275 average time/residue: 0.1466 time to fit residues: 61.6861 Evaluate side-chains 280 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 227 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain A residue 3244 LEU Chi-restraints excluded: chain A residue 3247 GLN Chi-restraints excluded: chain A residue 3307 VAL Chi-restraints excluded: chain A residue 3311 VAL Chi-restraints excluded: chain A residue 3315 VAL Chi-restraints excluded: chain A residue 3409 ILE Chi-restraints excluded: chain A residue 3528 GLU Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3554 THR Chi-restraints excluded: chain A residue 3566 ILE Chi-restraints excluded: chain A residue 3581 LEU Chi-restraints excluded: chain A residue 3625 THR Chi-restraints excluded: chain A residue 3627 VAL Chi-restraints excluded: chain A residue 3761 GLU Chi-restraints excluded: chain A residue 3832 ASP Chi-restraints excluded: chain A residue 3869 SER Chi-restraints excluded: chain A residue 3959 TRP Chi-restraints excluded: chain A residue 3963 ASP Chi-restraints excluded: chain A residue 3979 ILE Chi-restraints excluded: chain A residue 4024 ILE Chi-restraints excluded: chain A residue 4126 ASN Chi-restraints excluded: chain A residue 4193 SER Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4230 THR Chi-restraints excluded: chain A residue 4327 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain B residue 3244 LEU Chi-restraints excluded: chain B residue 3247 GLN Chi-restraints excluded: chain B residue 3272 LEU Chi-restraints excluded: chain B residue 3307 VAL Chi-restraints excluded: chain B residue 3311 VAL Chi-restraints excluded: chain B residue 3409 ILE Chi-restraints excluded: chain B residue 3528 GLU Chi-restraints excluded: chain B residue 3550 ILE Chi-restraints excluded: chain B residue 3581 LEU Chi-restraints excluded: chain B residue 3627 VAL Chi-restraints excluded: chain B residue 3761 GLU Chi-restraints excluded: chain B residue 3832 ASP Chi-restraints excluded: chain B residue 3959 TRP Chi-restraints excluded: chain B residue 3963 ASP Chi-restraints excluded: chain B residue 3968 LEU Chi-restraints excluded: chain B residue 3979 ILE Chi-restraints excluded: chain B residue 4024 ILE Chi-restraints excluded: chain B residue 4077 ILE Chi-restraints excluded: chain B residue 4223 LEU Chi-restraints excluded: chain B residue 4277 VAL Chi-restraints excluded: chain B residue 4327 THR Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain F residue 19 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 0.0570 chunk 209 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 205 optimal weight: 3.9990 chunk 198 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.150570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.103615 restraints weight = 26634.356| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.07 r_work: 0.3100 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18870 Z= 0.169 Angle : 0.528 13.327 25548 Z= 0.268 Chirality : 0.038 0.147 3026 Planarity : 0.004 0.041 3230 Dihedral : 4.341 59.162 2601 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.68 % Allowed : 16.51 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.18), residues: 2366 helix: 2.56 (0.13), residues: 1598 sheet: 1.35 (0.59), residues: 94 loop : -0.47 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B3252 TYR 0.014 0.001 TYR B4101 PHE 0.009 0.001 PHE A3293 TRP 0.021 0.002 TRP B4103 HIS 0.008 0.001 HIS A3429 Details of bonding type rmsd covalent geometry : bond 0.00412 (18862) covalent geometry : angle 0.52640 (25536) hydrogen bonds : bond 0.04593 ( 1214) hydrogen bonds : angle 3.27529 ( 3630) metal coordination : bond 0.00254 ( 8) metal coordination : angle 1.84285 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 235 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: E 30 THR cc_start: 0.6959 (p) cc_final: 0.6379 (p) REVERT: E 31 LYS cc_start: 0.7497 (ttmm) cc_final: 0.6340 (mmtm) REVERT: E 46 GLU cc_start: 0.7005 (tt0) cc_final: 0.6362 (tp30) REVERT: A 3247 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.7427 (mp10) REVERT: A 3528 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: A 3554 THR cc_start: 0.7120 (OUTLIER) cc_final: 0.6738 (m) REVERT: A 3832 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8033 (t0) REVERT: A 3963 ASP cc_start: 0.5728 (OUTLIER) cc_final: 0.5383 (t0) REVERT: A 4502 ARG cc_start: 0.6068 (ptt-90) cc_final: 0.5245 (ttp80) REVERT: C 330 ARG cc_start: 0.6805 (ptp-110) cc_final: 0.6538 (ttm110) REVERT: B 3231 HIS cc_start: 0.8000 (t70) cc_final: 0.7770 (t70) REVERT: B 3528 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7244 (mp0) REVERT: B 3530 ASP cc_start: 0.7267 (t0) cc_final: 0.7056 (t0) REVERT: B 3546 LYS cc_start: 0.7640 (pttp) cc_final: 0.7195 (mttp) REVERT: B 3614 LYS cc_start: 0.8457 (tptm) cc_final: 0.7947 (mmmt) REVERT: B 3754 MET cc_start: 0.8623 (mmm) cc_final: 0.8375 (mmm) REVERT: B 3829 LEU cc_start: 0.9039 (tp) cc_final: 0.8768 (tt) REVERT: B 3832 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8054 (t0) REVERT: B 3959 TRP cc_start: 0.6641 (OUTLIER) cc_final: 0.6242 (t60) REVERT: B 3963 ASP cc_start: 0.5517 (OUTLIER) cc_final: 0.5301 (t0) REVERT: B 4101 TYR cc_start: 0.7595 (m-80) cc_final: 0.7375 (m-80) REVERT: B 4229 SER cc_start: 0.8404 (m) cc_final: 0.8173 (t) REVERT: B 4498 PHE cc_start: 0.4954 (t80) cc_final: 0.4566 (t80) REVERT: F 46 GLU cc_start: 0.7673 (tp30) cc_final: 0.7411 (tp30) REVERT: F 50 GLN cc_start: 0.6662 (mm-40) cc_final: 0.5986 (mm-40) outliers start: 72 outliers final: 60 residues processed: 285 average time/residue: 0.1422 time to fit residues: 62.5771 Evaluate side-chains 298 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 229 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain A residue 3238 ARG Chi-restraints excluded: chain A residue 3243 LEU Chi-restraints excluded: chain A residue 3244 LEU Chi-restraints excluded: chain A residue 3247 GLN Chi-restraints excluded: chain A residue 3282 ILE Chi-restraints excluded: chain A residue 3307 VAL Chi-restraints excluded: chain A residue 3311 VAL Chi-restraints excluded: chain A residue 3315 VAL Chi-restraints excluded: chain A residue 3409 ILE Chi-restraints excluded: chain A residue 3458 LEU Chi-restraints excluded: chain A residue 3528 GLU Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3550 ILE Chi-restraints excluded: chain A residue 3554 THR Chi-restraints excluded: chain A residue 3566 ILE Chi-restraints excluded: chain A residue 3581 LEU Chi-restraints excluded: chain A residue 3605 LEU Chi-restraints excluded: chain A residue 3625 THR Chi-restraints excluded: chain A residue 3627 VAL Chi-restraints excluded: chain A residue 3747 ASP Chi-restraints excluded: chain A residue 3832 ASP Chi-restraints excluded: chain A residue 3869 SER Chi-restraints excluded: chain A residue 3959 TRP Chi-restraints excluded: chain A residue 3963 ASP Chi-restraints excluded: chain A residue 3979 ILE Chi-restraints excluded: chain A residue 3980 SER Chi-restraints excluded: chain A residue 4024 ILE Chi-restraints excluded: chain A residue 4126 ASN Chi-restraints excluded: chain A residue 4186 LEU Chi-restraints excluded: chain A residue 4193 SER Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4230 THR Chi-restraints excluded: chain A residue 4232 LEU Chi-restraints excluded: chain A residue 4277 VAL Chi-restraints excluded: chain A residue 4327 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain B residue 3243 LEU Chi-restraints excluded: chain B residue 3244 LEU Chi-restraints excluded: chain B residue 3272 LEU Chi-restraints excluded: chain B residue 3307 VAL Chi-restraints excluded: chain B residue 3311 VAL Chi-restraints excluded: chain B residue 3409 ILE Chi-restraints excluded: chain B residue 3458 LEU Chi-restraints excluded: chain B residue 3528 GLU Chi-restraints excluded: chain B residue 3550 ILE Chi-restraints excluded: chain B residue 3566 ILE Chi-restraints excluded: chain B residue 3581 LEU Chi-restraints excluded: chain B residue 3605 LEU Chi-restraints excluded: chain B residue 3627 VAL Chi-restraints excluded: chain B residue 3747 ASP Chi-restraints excluded: chain B residue 3832 ASP Chi-restraints excluded: chain B residue 3867 THR Chi-restraints excluded: chain B residue 3869 SER Chi-restraints excluded: chain B residue 3871 LYS Chi-restraints excluded: chain B residue 3959 TRP Chi-restraints excluded: chain B residue 3963 ASP Chi-restraints excluded: chain B residue 3968 LEU Chi-restraints excluded: chain B residue 3979 ILE Chi-restraints excluded: chain B residue 4024 ILE Chi-restraints excluded: chain B residue 4077 ILE Chi-restraints excluded: chain B residue 4223 LEU Chi-restraints excluded: chain B residue 4277 VAL Chi-restraints excluded: chain B residue 4327 THR Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain F residue 19 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 177 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 168 optimal weight: 0.3980 chunk 144 optimal weight: 0.7980 chunk 175 optimal weight: 0.7980 chunk 149 optimal weight: 8.9990 chunk 134 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 211 optimal weight: 0.1980 chunk 130 optimal weight: 0.0170 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.154592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.109856 restraints weight = 26430.380| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.25 r_work: 0.3164 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18870 Z= 0.093 Angle : 0.463 11.475 25548 Z= 0.236 Chirality : 0.035 0.135 3026 Planarity : 0.003 0.041 3230 Dihedral : 3.969 51.884 2601 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.86 % Allowed : 17.64 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.91 (0.18), residues: 2366 helix: 2.86 (0.13), residues: 1604 sheet: 1.17 (0.57), residues: 98 loop : -0.37 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3252 TYR 0.014 0.001 TYR B4101 PHE 0.010 0.001 PHE A3293 TRP 0.021 0.001 TRP A4103 HIS 0.005 0.001 HIS A3958 Details of bonding type rmsd covalent geometry : bond 0.00205 (18862) covalent geometry : angle 0.46279 (25536) hydrogen bonds : bond 0.03206 ( 1214) hydrogen bonds : angle 3.01048 ( 3630) metal coordination : bond 0.00079 ( 8) metal coordination : angle 0.43672 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 237 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: E 30 THR cc_start: 0.6828 (p) cc_final: 0.6332 (p) REVERT: E 31 LYS cc_start: 0.7263 (ttmm) cc_final: 0.6297 (mmtm) REVERT: E 46 GLU cc_start: 0.6714 (tt0) cc_final: 0.6115 (tp30) REVERT: A 3247 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.7363 (mp10) REVERT: A 3528 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7352 (mp0) REVERT: A 3554 THR cc_start: 0.7183 (t) cc_final: 0.6912 (m) REVERT: A 3832 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.8005 (t0) REVERT: A 4502 ARG cc_start: 0.6012 (ptt-90) cc_final: 0.5219 (ttp80) REVERT: C 330 ARG cc_start: 0.7051 (ptp-110) cc_final: 0.6685 (ttm110) REVERT: B 3231 HIS cc_start: 0.7960 (t70) cc_final: 0.7731 (t70) REVERT: B 3247 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.7207 (mp10) REVERT: B 3528 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7278 (mp0) REVERT: B 3530 ASP cc_start: 0.7151 (t0) cc_final: 0.6928 (t0) REVERT: B 3546 LYS cc_start: 0.7669 (pttp) cc_final: 0.7227 (mttp) REVERT: B 3614 LYS cc_start: 0.8490 (tptm) cc_final: 0.8103 (mmmt) REVERT: B 3829 LEU cc_start: 0.9005 (tp) cc_final: 0.8726 (tt) REVERT: B 3832 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.8004 (t0) REVERT: B 3959 TRP cc_start: 0.6311 (OUTLIER) cc_final: 0.6086 (t60) REVERT: B 4101 TYR cc_start: 0.7526 (m-80) cc_final: 0.7277 (m-80) REVERT: B 4229 SER cc_start: 0.8401 (m) cc_final: 0.8118 (t) REVERT: B 4498 PHE cc_start: 0.4834 (t80) cc_final: 0.4450 (t80) REVERT: F 46 GLU cc_start: 0.7573 (tp30) cc_final: 0.7246 (tp30) REVERT: F 50 GLN cc_start: 0.6558 (mm-40) cc_final: 0.5748 (mm-40) outliers start: 56 outliers final: 40 residues processed: 275 average time/residue: 0.1537 time to fit residues: 65.6527 Evaluate side-chains 277 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 230 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain A residue 3244 LEU Chi-restraints excluded: chain A residue 3247 GLN Chi-restraints excluded: chain A residue 3307 VAL Chi-restraints excluded: chain A residue 3311 VAL Chi-restraints excluded: chain A residue 3315 VAL Chi-restraints excluded: chain A residue 3458 LEU Chi-restraints excluded: chain A residue 3528 GLU Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3566 ILE Chi-restraints excluded: chain A residue 3581 LEU Chi-restraints excluded: chain A residue 3625 THR Chi-restraints excluded: chain A residue 3627 VAL Chi-restraints excluded: chain A residue 3761 GLU Chi-restraints excluded: chain A residue 3832 ASP Chi-restraints excluded: chain A residue 3959 TRP Chi-restraints excluded: chain A residue 3979 ILE Chi-restraints excluded: chain A residue 4024 ILE Chi-restraints excluded: chain A residue 4126 ASN Chi-restraints excluded: chain A residue 4193 SER Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4230 THR Chi-restraints excluded: chain A residue 4327 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain B residue 3244 LEU Chi-restraints excluded: chain B residue 3247 GLN Chi-restraints excluded: chain B residue 3307 VAL Chi-restraints excluded: chain B residue 3311 VAL Chi-restraints excluded: chain B residue 3458 LEU Chi-restraints excluded: chain B residue 3528 GLU Chi-restraints excluded: chain B residue 3566 ILE Chi-restraints excluded: chain B residue 3627 VAL Chi-restraints excluded: chain B residue 3761 GLU Chi-restraints excluded: chain B residue 3832 ASP Chi-restraints excluded: chain B residue 3871 LYS Chi-restraints excluded: chain B residue 3959 TRP Chi-restraints excluded: chain B residue 3968 LEU Chi-restraints excluded: chain B residue 3980 SER Chi-restraints excluded: chain B residue 4024 ILE Chi-restraints excluded: chain B residue 4223 LEU Chi-restraints excluded: chain B residue 4277 VAL Chi-restraints excluded: chain B residue 4327 THR Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain F residue 19 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 124 optimal weight: 5.9990 chunk 144 optimal weight: 0.7980 chunk 154 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 233 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.153583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.107967 restraints weight = 26514.336| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.23 r_work: 0.3139 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 0.042 18870 Z= 0.109 Angle : 0.492 13.545 25548 Z= 0.247 Chirality : 0.036 0.144 3026 Planarity : 0.003 0.041 3230 Dihedral : 3.994 52.380 2601 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.61 % Allowed : 17.89 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.18), residues: 2366 helix: 2.79 (0.13), residues: 1616 sheet: 1.26 (0.58), residues: 98 loop : -0.38 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3252 TYR 0.012 0.001 TYR B4101 PHE 0.011 0.001 PHE A4512 TRP 0.023 0.001 TRP B4103 HIS 0.006 0.001 HIS A3429 Details of bonding type rmsd covalent geometry : bond 0.00256 (18862) covalent geometry : angle 0.49192 (25536) hydrogen bonds : bond 0.03571 ( 1214) hydrogen bonds : angle 3.06393 ( 3630) metal coordination : bond 0.00124 ( 8) metal coordination : angle 1.10942 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 232 time to evaluate : 0.794 Fit side-chains REVERT: E 30 THR cc_start: 0.6895 (p) cc_final: 0.6344 (p) REVERT: E 31 LYS cc_start: 0.6978 (ttmm) cc_final: 0.6066 (mmtm) REVERT: E 50 GLN cc_start: 0.6559 (mm-40) cc_final: 0.6210 (mm-40) REVERT: A 3247 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.7330 (mp10) REVERT: A 3528 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7350 (mp0) REVERT: A 3554 THR cc_start: 0.7163 (t) cc_final: 0.6808 (m) REVERT: A 3832 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.8019 (t0) REVERT: A 4502 ARG cc_start: 0.6051 (ptt-90) cc_final: 0.5192 (ttp80) REVERT: C 330 ARG cc_start: 0.7055 (ptp-110) cc_final: 0.6689 (ttm110) REVERT: B 3231 HIS cc_start: 0.7978 (t70) cc_final: 0.7737 (t70) REVERT: B 3247 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.7277 (mp10) REVERT: B 3528 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: B 3530 ASP cc_start: 0.7194 (t0) cc_final: 0.6969 (t0) REVERT: B 3546 LYS cc_start: 0.7589 (pttp) cc_final: 0.7172 (mttt) REVERT: B 3614 LYS cc_start: 0.8501 (tptm) cc_final: 0.8050 (mmmt) REVERT: B 3829 LEU cc_start: 0.9013 (tp) cc_final: 0.8733 (tt) REVERT: B 3832 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.8013 (t0) REVERT: B 3959 TRP cc_start: 0.6374 (OUTLIER) cc_final: 0.6143 (t60) REVERT: B 4101 TYR cc_start: 0.7482 (m-80) cc_final: 0.7256 (m-80) REVERT: B 4229 SER cc_start: 0.8420 (m) cc_final: 0.8126 (t) REVERT: B 4498 PHE cc_start: 0.4862 (t80) cc_final: 0.4478 (t80) REVERT: F 46 GLU cc_start: 0.7686 (tp30) cc_final: 0.7389 (tp30) REVERT: F 50 GLN cc_start: 0.5898 (mm-40) cc_final: 0.5207 (mm-40) REVERT: F 55 GLU cc_start: 0.4264 (tt0) cc_final: 0.3850 (tm-30) outliers start: 51 outliers final: 41 residues processed: 270 average time/residue: 0.1529 time to fit residues: 63.2098 Evaluate side-chains 277 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 229 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain A residue 3244 LEU Chi-restraints excluded: chain A residue 3247 GLN Chi-restraints excluded: chain A residue 3307 VAL Chi-restraints excluded: chain A residue 3311 VAL Chi-restraints excluded: chain A residue 3315 VAL Chi-restraints excluded: chain A residue 3458 LEU Chi-restraints excluded: chain A residue 3528 GLU Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3566 ILE Chi-restraints excluded: chain A residue 3581 LEU Chi-restraints excluded: chain A residue 3625 THR Chi-restraints excluded: chain A residue 3627 VAL Chi-restraints excluded: chain A residue 3832 ASP Chi-restraints excluded: chain A residue 3959 TRP Chi-restraints excluded: chain A residue 3979 ILE Chi-restraints excluded: chain A residue 4024 ILE Chi-restraints excluded: chain A residue 4126 ASN Chi-restraints excluded: chain A residue 4193 SER Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4230 THR Chi-restraints excluded: chain A residue 4327 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain B residue 3244 LEU Chi-restraints excluded: chain B residue 3247 GLN Chi-restraints excluded: chain B residue 3307 VAL Chi-restraints excluded: chain B residue 3311 VAL Chi-restraints excluded: chain B residue 3458 LEU Chi-restraints excluded: chain B residue 3528 GLU Chi-restraints excluded: chain B residue 3566 ILE Chi-restraints excluded: chain B residue 3581 LEU Chi-restraints excluded: chain B residue 3627 VAL Chi-restraints excluded: chain B residue 3832 ASP Chi-restraints excluded: chain B residue 3869 SER Chi-restraints excluded: chain B residue 3871 LYS Chi-restraints excluded: chain B residue 3959 TRP Chi-restraints excluded: chain B residue 3968 LEU Chi-restraints excluded: chain B residue 3979 ILE Chi-restraints excluded: chain B residue 3980 SER Chi-restraints excluded: chain B residue 4024 ILE Chi-restraints excluded: chain B residue 4223 LEU Chi-restraints excluded: chain B residue 4277 VAL Chi-restraints excluded: chain B residue 4327 THR Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain F residue 19 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 88 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 239 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 228 optimal weight: 10.0000 chunk 231 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 223 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3639 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.153561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.109011 restraints weight = 26522.070| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.39 r_work: 0.3132 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18870 Z= 0.112 Angle : 0.496 13.898 25548 Z= 0.248 Chirality : 0.036 0.135 3026 Planarity : 0.003 0.041 3230 Dihedral : 4.009 52.726 2601 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.56 % Allowed : 17.94 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.83 (0.18), residues: 2366 helix: 2.77 (0.13), residues: 1614 sheet: 1.15 (0.56), residues: 98 loop : -0.37 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3252 TYR 0.013 0.001 TYR B4101 PHE 0.014 0.001 PHE B4512 TRP 0.024 0.001 TRP B4103 HIS 0.006 0.001 HIS A3429 Details of bonding type rmsd covalent geometry : bond 0.00264 (18862) covalent geometry : angle 0.49515 (25536) hydrogen bonds : bond 0.03599 ( 1214) hydrogen bonds : angle 3.06869 ( 3630) metal coordination : bond 0.00117 ( 8) metal coordination : angle 1.04902 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 231 time to evaluate : 0.747 Fit side-chains REVERT: E 30 THR cc_start: 0.6961 (p) cc_final: 0.6363 (p) REVERT: E 31 LYS cc_start: 0.6795 (ttmm) cc_final: 0.5996 (mmtm) REVERT: E 50 GLN cc_start: 0.5940 (mm-40) cc_final: 0.5549 (mm-40) REVERT: A 3247 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7356 (mp10) REVERT: A 3528 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: A 3554 THR cc_start: 0.7263 (t) cc_final: 0.7045 (m) REVERT: A 3832 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.8019 (t0) REVERT: A 4502 ARG cc_start: 0.5999 (ptt-90) cc_final: 0.5193 (ttp80) REVERT: C 330 ARG cc_start: 0.6939 (ptp-110) cc_final: 0.6578 (ttm110) REVERT: B 3231 HIS cc_start: 0.8061 (t70) cc_final: 0.7824 (t70) REVERT: B 3247 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.7269 (mp10) REVERT: B 3528 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7275 (mp0) REVERT: B 3530 ASP cc_start: 0.7202 (t0) cc_final: 0.6979 (t0) REVERT: B 3546 LYS cc_start: 0.7644 (pttp) cc_final: 0.7186 (mttp) REVERT: B 3614 LYS cc_start: 0.8508 (tptm) cc_final: 0.8055 (mmmt) REVERT: B 3829 LEU cc_start: 0.9007 (tp) cc_final: 0.8726 (tt) REVERT: B 3832 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.8020 (t0) REVERT: B 3959 TRP cc_start: 0.6366 (OUTLIER) cc_final: 0.6111 (t60) REVERT: B 4101 TYR cc_start: 0.7513 (m-80) cc_final: 0.7276 (m-80) REVERT: B 4229 SER cc_start: 0.8420 (m) cc_final: 0.8112 (t) REVERT: B 4498 PHE cc_start: 0.5054 (t80) cc_final: 0.4671 (t80) REVERT: F 46 GLU cc_start: 0.7710 (tp30) cc_final: 0.7389 (tp30) REVERT: F 50 GLN cc_start: 0.5936 (mm-40) cc_final: 0.5237 (mm110) REVERT: F 55 GLU cc_start: 0.4141 (tt0) cc_final: 0.3757 (tm-30) outliers start: 50 outliers final: 42 residues processed: 268 average time/residue: 0.1388 time to fit residues: 57.3513 Evaluate side-chains 278 residues out of total 2134 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 229 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain A residue 3244 LEU Chi-restraints excluded: chain A residue 3247 GLN Chi-restraints excluded: chain A residue 3307 VAL Chi-restraints excluded: chain A residue 3311 VAL Chi-restraints excluded: chain A residue 3315 VAL Chi-restraints excluded: chain A residue 3458 LEU Chi-restraints excluded: chain A residue 3528 GLU Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3566 ILE Chi-restraints excluded: chain A residue 3581 LEU Chi-restraints excluded: chain A residue 3605 LEU Chi-restraints excluded: chain A residue 3625 THR Chi-restraints excluded: chain A residue 3627 VAL Chi-restraints excluded: chain A residue 3832 ASP Chi-restraints excluded: chain A residue 3959 TRP Chi-restraints excluded: chain A residue 3979 ILE Chi-restraints excluded: chain A residue 4024 ILE Chi-restraints excluded: chain A residue 4126 ASN Chi-restraints excluded: chain A residue 4193 SER Chi-restraints excluded: chain A residue 4223 LEU Chi-restraints excluded: chain A residue 4230 THR Chi-restraints excluded: chain A residue 4277 VAL Chi-restraints excluded: chain A residue 4327 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain B residue 3244 LEU Chi-restraints excluded: chain B residue 3247 GLN Chi-restraints excluded: chain B residue 3307 VAL Chi-restraints excluded: chain B residue 3311 VAL Chi-restraints excluded: chain B residue 3458 LEU Chi-restraints excluded: chain B residue 3528 GLU Chi-restraints excluded: chain B residue 3566 ILE Chi-restraints excluded: chain B residue 3627 VAL Chi-restraints excluded: chain B residue 3832 ASP Chi-restraints excluded: chain B residue 3869 SER Chi-restraints excluded: chain B residue 3871 LYS Chi-restraints excluded: chain B residue 3959 TRP Chi-restraints excluded: chain B residue 3968 LEU Chi-restraints excluded: chain B residue 3979 ILE Chi-restraints excluded: chain B residue 3980 SER Chi-restraints excluded: chain B residue 4024 ILE Chi-restraints excluded: chain B residue 4223 LEU Chi-restraints excluded: chain B residue 4277 VAL Chi-restraints excluded: chain B residue 4327 THR Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain F residue 19 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 39 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 232 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 131 optimal weight: 0.0870 chunk 16 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 overall best weight: 1.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.150932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.104104 restraints weight = 26642.898| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.06 r_work: 0.3106 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18870 Z= 0.165 Angle : 0.541 13.530 25548 Z= 0.272 Chirality : 0.038 0.143 3026 Planarity : 0.004 0.041 3230 Dihedral : 4.259 58.899 2601 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.86 % Allowed : 17.79 % Favored : 79.35 % 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: 2.62 (0.18), residues: 2366 helix: 2.62 (0.13), residues: 1608 sheet: 1.06 (0.56), residues: 98 loop : -0.45 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B3252 TYR 0.015 0.001 TYR B4101 PHE 0.011 0.001 PHE A4512 TRP 0.025 0.002 TRP B4103 HIS 0.007 0.001 HIS A3429 Details of bonding type rmsd covalent geometry : bond 0.00403 (18862) covalent geometry : angle 0.53955 (25536) hydrogen bonds : bond 0.04394 ( 1214) hydrogen bonds : angle 3.22914 ( 3630) metal coordination : bond 0.00269 ( 8) metal coordination : angle 1.76029 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6078.12 seconds wall clock time: 104 minutes 36.74 seconds (6276.74 seconds total)