Starting phenix.real_space_refine on Fri Jul 3 20:40:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8drp_27680/07_2026/8drp_27680.cif Found real_map, /net/cci-nas-00/data/ceres_data/8drp_27680/07_2026/8drp_27680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8drp_27680/07_2026/8drp_27680.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8drp_27680/07_2026/8drp_27680.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8drp_27680/07_2026/8drp_27680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8drp_27680/07_2026/8drp_27680.map" model { file = "/net/cci-nas-00/data/ceres_data/8drp_27680/07_2026/8drp_27680.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8drp_27680/07_2026/8drp_27680.cif" } resolution = 2.84 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= 0.002 sd= 0.091 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 12 5.49 5 S 104 5.16 5 C 10444 2.51 5 N 2564 2.21 5 O 2688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15816 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3908 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 13, 'TRANS': 498} Chain breaks: 4 Unresolved non-hydrogen bonds: 332 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 267 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 31, 'ASP:plan': 18, 'TRP:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 241 Chain: "B" Number of atoms: 3908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3908 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 13, 'TRANS': 498} Chain breaks: 4 Unresolved non-hydrogen bonds: 332 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 267 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 31, 'ASP:plan': 18, 'TRP:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 241 Chain: "C" Number of atoms: 3908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3908 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 13, 'TRANS': 498} Chain breaks: 4 Unresolved non-hydrogen bonds: 332 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 267 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 31, 'ASP:plan': 18, 'TRP:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 241 Chain: "D" Number of atoms: 3908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3908 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 13, 'TRANS': 498} Chain breaks: 4 Unresolved non-hydrogen bonds: 332 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 267 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 31, 'ASP:plan': 18, 'TRP:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 241 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' ZN': 1, 'ATP': 1, 'CFF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' ZN': 1, 'ATP': 1, 'CFF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' ZN': 1, 'ATP': 1, 'CFF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' ZN': 1, 'ATP': 1, 'CFF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3304 SG CYS A4958 52.160 71.994 24.915 1.00 58.39 S ATOM 3329 SG CYS A4961 52.612 70.689 21.409 1.00 57.00 S ATOM 7212 SG CYS B4958 73.526 52.160 24.915 1.00 58.39 S ATOM 7237 SG CYS B4961 74.831 52.612 21.409 1.00 57.00 S ATOM 11120 SG CYS C4958 93.359 73.527 24.915 1.00 58.39 S ATOM 11145 SG CYS C4961 92.907 74.832 21.409 1.00 57.00 S ATOM 15028 SG CYS D4958 71.993 93.361 24.915 1.00 58.39 S ATOM 15053 SG CYS D4961 70.688 92.909 21.409 1.00 57.00 S Time building chain proxies: 3.32, per 1000 atoms: 0.21 Number of scatterers: 15816 At special positions: 0 Unit cell: (146.59, 146.59, 109.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 104 16.00 P 12 15.00 O 2688 8.00 N 2564 7.00 C 10444 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A4876 " - pdb=" SG CYS A4882 " distance=2.01 Simple disulfide: pdb=" SG CYS B4876 " - pdb=" SG CYS B4882 " distance=2.01 Simple disulfide: pdb=" SG CYS C4876 " - pdb=" SG CYS C4882 " distance=2.01 Simple disulfide: pdb=" SG CYS D4876 " - pdb=" SG CYS D4882 " distance=2.01 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: 1.27 Conformation dependent library (CDL) restraints added in 688.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5103 " pdb="ZN ZN A5103 " - pdb=" NE2 HIS A4978 " pdb="ZN ZN A5103 " - pdb=" ND1 HIS A4983 " pdb="ZN ZN A5103 " - pdb=" SG CYS A4961 " pdb="ZN ZN A5103 " - pdb=" SG CYS A4958 " pdb=" ZN B5103 " pdb="ZN ZN B5103 " - pdb=" NE2 HIS B4978 " pdb="ZN ZN B5103 " - pdb=" ND1 HIS B4983 " pdb="ZN ZN B5103 " - pdb=" SG CYS B4961 " pdb="ZN ZN B5103 " - pdb=" SG CYS B4958 " pdb=" ZN C5103 " pdb="ZN ZN C5103 " - pdb=" NE2 HIS C4978 " pdb="ZN ZN C5103 " - pdb=" ND1 HIS C4983 " pdb="ZN ZN C5103 " - pdb=" SG CYS C4961 " pdb="ZN ZN C5103 " - pdb=" SG CYS C4958 " pdb=" ZN D5103 " pdb="ZN ZN D5103 " - pdb=" NE2 HIS D4978 " pdb="ZN ZN D5103 " - pdb=" ND1 HIS D4983 " pdb="ZN ZN D5103 " - pdb=" SG CYS D4961 " pdb="ZN ZN D5103 " - pdb=" SG CYS D4958 " Number of angles added : 4 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3864 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 8 sheets defined 74.6% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 4198 through 4205 removed outlier: 3.568A pdb=" N ARG A4202 " --> pdb=" O SER A4198 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP A4205 " --> pdb=" O ASN A4201 " (cutoff:3.500A) Processing helix chain 'A' and resid 4207 through 4225 Processing helix chain 'A' and resid 4229 through 4252 Processing helix chain 'A' and resid 4324 through 4341 Processing helix chain 'A' and resid 4542 through 4558 removed outlier: 3.635A pdb=" N ASN A4558 " --> pdb=" O TYR A4554 " (cutoff:3.500A) Processing helix chain 'A' and resid 4559 through 4578 Processing helix chain 'A' and resid 4638 through 4665 Processing helix chain 'A' and resid 4665 through 4684 Processing helix chain 'A' and resid 4696 through 4702 Processing helix chain 'A' and resid 4703 through 4708 removed outlier: 3.621A pdb=" N LEU A4706 " --> pdb=" O ARG A4703 " (cutoff:3.500A) Processing helix chain 'A' and resid 4767 through 4771 Processing helix chain 'A' and resid 4772 through 4785 Processing helix chain 'A' and resid 4786 through 4805 removed outlier: 3.843A pdb=" N HIS A4803 " --> pdb=" O SER A4799 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) Processing helix chain 'A' and resid 4806 through 4813 removed outlier: 3.504A pdb=" N ALA A4811 " --> pdb=" O PHE A4808 " (cutoff:3.500A) Processing helix chain 'A' and resid 4814 through 4820 Processing helix chain 'A' and resid 4820 through 4833 removed outlier: 3.782A pdb=" N VAL A4830 " --> pdb=" O ILE A4826 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR A4831 " --> pdb=" O LEU A4827 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASN A4833 " --> pdb=" O SER A4829 " (cutoff:3.500A) Processing helix chain 'A' and resid 4833 through 4859 Processing helix chain 'A' and resid 4860 through 4863 Processing helix chain 'A' and resid 4878 through 4894 removed outlier: 4.654A pdb=" N VAL A4891 " --> pdb=" O MET A4887 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG A4892 " --> pdb=" O TYR A4888 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLY A4894 " --> pdb=" O GLY A4890 " (cutoff:3.500A) Processing helix chain 'A' and resid 4909 through 4926 Processing helix chain 'A' and resid 4927 through 4957 Processing helix chain 'A' and resid 4964 through 4970 removed outlier: 3.975A pdb=" N PHE A4968 " --> pdb=" O GLY A4964 " (cutoff:3.500A) Processing helix chain 'A' and resid 4973 through 4981 Processing helix chain 'A' and resid 4984 through 4998 Processing helix chain 'A' and resid 5004 through 5016 Processing helix chain 'A' and resid 5027 through 5032 Processing helix chain 'B' and resid 4198 through 4205 removed outlier: 3.568A pdb=" N ARG B4202 " --> pdb=" O SER B4198 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP B4205 " --> pdb=" O ASN B4201 " (cutoff:3.500A) Processing helix chain 'B' and resid 4207 through 4225 Processing helix chain 'B' and resid 4229 through 4252 Processing helix chain 'B' and resid 4324 through 4341 removed outlier: 3.506A pdb=" N VAL B4338 " --> pdb=" O LEU B4334 " (cutoff:3.500A) Processing helix chain 'B' and resid 4542 through 4558 removed outlier: 3.635A pdb=" N ASN B4558 " --> pdb=" O TYR B4554 " (cutoff:3.500A) Processing helix chain 'B' and resid 4559 through 4578 Processing helix chain 'B' and resid 4638 through 4665 Processing helix chain 'B' and resid 4665 through 4684 Processing helix chain 'B' and resid 4696 through 4702 Processing helix chain 'B' and resid 4703 through 4708 removed outlier: 3.621A pdb=" N LEU B4706 " --> pdb=" O ARG B4703 " (cutoff:3.500A) Processing helix chain 'B' and resid 4767 through 4771 Processing helix chain 'B' and resid 4772 through 4785 Processing helix chain 'B' and resid 4786 through 4805 removed outlier: 3.843A pdb=" N HIS B4803 " --> pdb=" O SER B4799 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR B4804 " --> pdb=" O LEU B4800 " (cutoff:3.500A) Processing helix chain 'B' and resid 4806 through 4813 removed outlier: 3.504A pdb=" N ALA B4811 " --> pdb=" O PHE B4808 " (cutoff:3.500A) Processing helix chain 'B' and resid 4814 through 4820 Processing helix chain 'B' and resid 4820 through 4833 removed outlier: 3.782A pdb=" N VAL B4830 " --> pdb=" O ILE B4826 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR B4831 " --> pdb=" O LEU B4827 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASN B4833 " --> pdb=" O SER B4829 " (cutoff:3.500A) Processing helix chain 'B' and resid 4833 through 4859 Processing helix chain 'B' and resid 4860 through 4863 Processing helix chain 'B' and resid 4878 through 4894 removed outlier: 4.654A pdb=" N VAL B4891 " --> pdb=" O MET B4887 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG B4892 " --> pdb=" O TYR B4888 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLY B4894 " --> pdb=" O GLY B4890 " (cutoff:3.500A) Processing helix chain 'B' and resid 4909 through 4926 Processing helix chain 'B' and resid 4927 through 4957 Processing helix chain 'B' and resid 4964 through 4970 removed outlier: 3.975A pdb=" N PHE B4968 " --> pdb=" O GLY B4964 " (cutoff:3.500A) Processing helix chain 'B' and resid 4973 through 4981 Processing helix chain 'B' and resid 4984 through 4998 Processing helix chain 'B' and resid 5004 through 5016 Processing helix chain 'B' and resid 5027 through 5032 Processing helix chain 'C' and resid 4198 through 4205 removed outlier: 3.568A pdb=" N ARG C4202 " --> pdb=" O SER C4198 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP C4205 " --> pdb=" O ASN C4201 " (cutoff:3.500A) Processing helix chain 'C' and resid 4207 through 4225 Processing helix chain 'C' and resid 4229 through 4252 Processing helix chain 'C' and resid 4324 through 4341 Processing helix chain 'C' and resid 4542 through 4558 removed outlier: 3.635A pdb=" N ASN C4558 " --> pdb=" O TYR C4554 " (cutoff:3.500A) Processing helix chain 'C' and resid 4559 through 4578 Processing helix chain 'C' and resid 4638 through 4665 Processing helix chain 'C' and resid 4665 through 4684 Processing helix chain 'C' and resid 4696 through 4702 Processing helix chain 'C' and resid 4703 through 4708 removed outlier: 3.621A pdb=" N LEU C4706 " --> pdb=" O ARG C4703 " (cutoff:3.500A) Processing helix chain 'C' and resid 4767 through 4771 Processing helix chain 'C' and resid 4772 through 4785 Processing helix chain 'C' and resid 4786 through 4805 removed outlier: 3.843A pdb=" N HIS C4803 " --> pdb=" O SER C4799 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR C4804 " --> pdb=" O LEU C4800 " (cutoff:3.500A) Processing helix chain 'C' and resid 4806 through 4813 removed outlier: 3.504A pdb=" N ALA C4811 " --> pdb=" O PHE C4808 " (cutoff:3.500A) Processing helix chain 'C' and resid 4814 through 4820 Processing helix chain 'C' and resid 4820 through 4833 removed outlier: 3.782A pdb=" N VAL C4830 " --> pdb=" O ILE C4826 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR C4831 " --> pdb=" O LEU C4827 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASN C4833 " --> pdb=" O SER C4829 " (cutoff:3.500A) Processing helix chain 'C' and resid 4833 through 4859 Processing helix chain 'C' and resid 4860 through 4863 Processing helix chain 'C' and resid 4878 through 4894 removed outlier: 4.654A pdb=" N VAL C4891 " --> pdb=" O MET C4887 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG C4892 " --> pdb=" O TYR C4888 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLY C4894 " --> pdb=" O GLY C4890 " (cutoff:3.500A) Processing helix chain 'C' and resid 4909 through 4926 Processing helix chain 'C' and resid 4927 through 4957 Processing helix chain 'C' and resid 4964 through 4970 removed outlier: 3.975A pdb=" N PHE C4968 " --> pdb=" O GLY C4964 " (cutoff:3.500A) Processing helix chain 'C' and resid 4973 through 4981 Processing helix chain 'C' and resid 4984 through 4998 Processing helix chain 'C' and resid 5004 through 5016 Processing helix chain 'C' and resid 5027 through 5032 Processing helix chain 'D' and resid 4198 through 4205 removed outlier: 3.568A pdb=" N ARG D4202 " --> pdb=" O SER D4198 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP D4205 " --> pdb=" O ASN D4201 " (cutoff:3.500A) Processing helix chain 'D' and resid 4207 through 4225 Processing helix chain 'D' and resid 4229 through 4252 Processing helix chain 'D' and resid 4324 through 4341 removed outlier: 3.506A pdb=" N VAL D4338 " --> pdb=" O LEU D4334 " (cutoff:3.500A) Processing helix chain 'D' and resid 4542 through 4558 removed outlier: 3.635A pdb=" N ASN D4558 " --> pdb=" O TYR D4554 " (cutoff:3.500A) Processing helix chain 'D' and resid 4559 through 4578 Processing helix chain 'D' and resid 4638 through 4665 Processing helix chain 'D' and resid 4665 through 4684 Processing helix chain 'D' and resid 4696 through 4702 Processing helix chain 'D' and resid 4703 through 4708 removed outlier: 3.621A pdb=" N LEU D4706 " --> pdb=" O ARG D4703 " (cutoff:3.500A) Processing helix chain 'D' and resid 4767 through 4771 Processing helix chain 'D' and resid 4772 through 4785 Processing helix chain 'D' and resid 4786 through 4805 removed outlier: 3.843A pdb=" N HIS D4803 " --> pdb=" O SER D4799 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR D4804 " --> pdb=" O LEU D4800 " (cutoff:3.500A) Processing helix chain 'D' and resid 4806 through 4813 removed outlier: 3.504A pdb=" N ALA D4811 " --> pdb=" O PHE D4808 " (cutoff:3.500A) Processing helix chain 'D' and resid 4814 through 4820 Processing helix chain 'D' and resid 4820 through 4833 removed outlier: 3.782A pdb=" N VAL D4830 " --> pdb=" O ILE D4826 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR D4831 " --> pdb=" O LEU D4827 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASN D4833 " --> pdb=" O SER D4829 " (cutoff:3.500A) Processing helix chain 'D' and resid 4833 through 4859 Processing helix chain 'D' and resid 4860 through 4863 Processing helix chain 'D' and resid 4878 through 4894 removed outlier: 4.654A pdb=" N VAL D4891 " --> pdb=" O MET D4887 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG D4892 " --> pdb=" O TYR D4888 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLY D4894 " --> pdb=" O GLY D4890 " (cutoff:3.500A) Processing helix chain 'D' and resid 4909 through 4926 Processing helix chain 'D' and resid 4927 through 4957 Processing helix chain 'D' and resid 4964 through 4970 removed outlier: 3.975A pdb=" N PHE D4968 " --> pdb=" O GLY D4964 " (cutoff:3.500A) Processing helix chain 'D' and resid 4973 through 4981 Processing helix chain 'D' and resid 4984 through 4998 Processing helix chain 'D' and resid 5004 through 5016 Processing helix chain 'D' and resid 5027 through 5032 Processing sheet with id=AA1, first strand: chain 'A' and resid 4178 through 4184 Processing sheet with id=AA2, first strand: chain 'A' and resid 4580 through 4583 Processing sheet with id=AA3, first strand: chain 'B' and resid 4178 through 4184 Processing sheet with id=AA4, first strand: chain 'B' and resid 4580 through 4583 Processing sheet with id=AA5, first strand: chain 'C' and resid 4178 through 4184 Processing sheet with id=AA6, first strand: chain 'C' and resid 4580 through 4583 Processing sheet with id=AA7, first strand: chain 'D' and resid 4178 through 4184 Processing sheet with id=AA8, first strand: chain 'D' and resid 4580 through 4583 1106 hydrogen bonds defined for protein. 3222 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2400 1.32 - 1.44: 4990 1.44 - 1.57: 8678 1.57 - 1.70: 20 1.70 - 1.82: 168 Bond restraints: 16256 Sorted by residual: bond pdb=" C TRP C4336 " pdb=" O TRP C4336 " ideal model delta sigma weight residual 1.237 1.194 0.043 1.17e-02 7.31e+03 1.36e+01 bond pdb=" N ASP C4878 " pdb=" CA ASP C4878 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.21e-02 6.83e+03 7.90e+00 bond pdb=" N ASP A4878 " pdb=" CA ASP A4878 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.21e-02 6.83e+03 7.90e+00 bond pdb=" N ASP B4878 " pdb=" CA ASP B4878 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.21e-02 6.83e+03 7.90e+00 bond pdb=" N ASP D4878 " pdb=" CA ASP D4878 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.21e-02 6.83e+03 7.90e+00 ... (remaining 16251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 21480 1.82 - 3.64: 542 3.64 - 5.46: 118 5.46 - 7.28: 20 7.28 - 9.10: 20 Bond angle restraints: 22180 Sorted by residual: angle pdb=" N CYS C4882 " pdb=" CA CYS C4882 " pdb=" C CYS C4882 " ideal model delta sigma weight residual 111.82 104.06 7.76 1.16e+00 7.43e-01 4.47e+01 angle pdb=" N CYS B4882 " pdb=" CA CYS B4882 " pdb=" C CYS B4882 " ideal model delta sigma weight residual 111.82 104.06 7.76 1.16e+00 7.43e-01 4.47e+01 angle pdb=" N CYS A4882 " pdb=" CA CYS A4882 " pdb=" C CYS A4882 " ideal model delta sigma weight residual 111.82 104.06 7.76 1.16e+00 7.43e-01 4.47e+01 angle pdb=" N CYS D4882 " pdb=" CA CYS D4882 " pdb=" C CYS D4882 " ideal model delta sigma weight residual 111.82 104.06 7.76 1.16e+00 7.43e-01 4.47e+01 angle pdb=" N PRO D4709 " pdb=" CA PRO D4709 " pdb=" C PRO D4709 " ideal model delta sigma weight residual 114.03 107.72 6.31 1.23e+00 6.61e-01 2.64e+01 ... (remaining 22175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 7808 15.93 - 31.86: 837 31.86 - 47.79: 355 47.79 - 63.72: 104 63.72 - 79.65: 20 Dihedral angle restraints: 9124 sinusoidal: 3120 harmonic: 6004 Sorted by residual: dihedral pdb=" CG ARG A4944 " pdb=" CD ARG A4944 " pdb=" NE ARG A4944 " pdb=" CZ ARG A4944 " ideal model delta sinusoidal sigma weight residual 90.00 131.71 -41.71 2 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CG ARG B4944 " pdb=" CD ARG B4944 " pdb=" NE ARG B4944 " pdb=" CZ ARG B4944 " ideal model delta sinusoidal sigma weight residual 90.00 131.71 -41.71 2 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CG ARG D4944 " pdb=" CD ARG D4944 " pdb=" NE ARG D4944 " pdb=" CZ ARG D4944 " ideal model delta sinusoidal sigma weight residual 90.00 131.71 -41.71 2 1.50e+01 4.44e-03 9.44e+00 ... (remaining 9121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1877 0.040 - 0.081: 454 0.081 - 0.121: 137 0.121 - 0.161: 12 0.161 - 0.202: 8 Chirality restraints: 2488 Sorted by residual: chirality pdb=" CB ILE A4183 " pdb=" CA ILE A4183 " pdb=" CG1 ILE A4183 " pdb=" CG2 ILE A4183 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB ILE C4183 " pdb=" CA ILE C4183 " pdb=" CG1 ILE C4183 " pdb=" CG2 ILE C4183 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB ILE B4183 " pdb=" CA ILE B4183 " pdb=" CG1 ILE B4183 " pdb=" CG2 ILE B4183 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 2485 not shown) Planarity restraints: 2736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A4878 " 0.013 2.00e-02 2.50e+03 2.76e-02 7.62e+00 pdb=" C ASP A4878 " -0.048 2.00e-02 2.50e+03 pdb=" O ASP A4878 " 0.018 2.00e-02 2.50e+03 pdb=" N MET A4879 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B4878 " 0.013 2.00e-02 2.50e+03 2.76e-02 7.62e+00 pdb=" C ASP B4878 " -0.048 2.00e-02 2.50e+03 pdb=" O ASP B4878 " 0.018 2.00e-02 2.50e+03 pdb=" N MET B4879 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D4878 " -0.013 2.00e-02 2.50e+03 2.76e-02 7.62e+00 pdb=" C ASP D4878 " 0.048 2.00e-02 2.50e+03 pdb=" O ASP D4878 " -0.018 2.00e-02 2.50e+03 pdb=" N MET D4879 " -0.016 2.00e-02 2.50e+03 ... (remaining 2733 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 4473 2.81 - 3.33: 15608 3.33 - 3.85: 27632 3.85 - 4.38: 29905 4.38 - 4.90: 51793 Nonbonded interactions: 129411 Sorted by model distance: nonbonded pdb=" OH TYR B4661 " pdb=" OD2 ASP B4786 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR D4661 " pdb=" OD2 ASP D4786 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR C4661 " pdb=" OD2 ASP C4786 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR A4661 " pdb=" OD2 ASP A4786 " model vdw 2.282 3.040 nonbonded pdb=" O CYS C4238 " pdb=" OG1 THR C4241 " model vdw 2.294 3.040 ... (remaining 129406 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.420 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16276 Z= 0.270 Angle : 0.711 9.101 22192 Z= 0.442 Chirality : 0.039 0.202 2488 Planarity : 0.004 0.036 2736 Dihedral : 16.938 79.647 5248 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.22 % Allowed : 26.58 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.19), residues: 2008 helix: 2.11 (0.13), residues: 1404 sheet: -0.18 (0.52), residues: 104 loop : -0.92 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A5029 TYR 0.018 0.001 TYR C5014 PHE 0.011 0.001 PHE D4711 TRP 0.011 0.001 TRP B4716 HIS 0.001 0.000 HIS B4978 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.27 (16256) covalent geometry : angle 0.70621 / 0.44 (22180) SS BOND : bond 0.01820 / 0.91 ( 4) SS BOND : angle 1.42130 / 1.00 ( 8) hydrogen bonds : bond 0.14263 / 9.81 ( 1106) hydrogen bonds : angle 5.00027 / 3.74 ( 3222) metal coordination : bond 0.00607 / 0.37 ( 16) metal coordination : angle 6.13153 / 4.30 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 292 time to evaluate : 0.423 Fit side-chains REVERT: A 4704 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6048 (tp) REVERT: A 4777 ILE cc_start: 0.7635 (mp) cc_final: 0.7416 (pt) REVERT: A 4778 TRP cc_start: 0.7384 (OUTLIER) cc_final: 0.6135 (t-100) REVERT: B 4704 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6043 (tp) REVERT: B 4777 ILE cc_start: 0.7632 (mp) cc_final: 0.7414 (pt) REVERT: B 4778 TRP cc_start: 0.7378 (OUTLIER) cc_final: 0.6133 (t-100) REVERT: C 4704 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6045 (tp) REVERT: C 4777 ILE cc_start: 0.7633 (mp) cc_final: 0.7414 (pt) REVERT: C 4778 TRP cc_start: 0.7380 (OUTLIER) cc_final: 0.6129 (t-100) REVERT: D 4704 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6042 (tp) REVERT: D 4777 ILE cc_start: 0.7639 (mp) cc_final: 0.7420 (pt) REVERT: D 4778 TRP cc_start: 0.7382 (OUTLIER) cc_final: 0.6128 (t-100) outliers start: 47 outliers final: 27 residues processed: 335 average time/residue: 0.4328 time to fit residues: 164.3873 Evaluate side-chains 324 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 289 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4236 SER Chi-restraints excluded: chain A residue 4246 GLN Chi-restraints excluded: chain A residue 4662 ASN Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4707 ASN Chi-restraints excluded: chain A residue 4778 TRP Chi-restraints excluded: chain A residue 4785 THR Chi-restraints excluded: chain A residue 5001 THR Chi-restraints excluded: chain B residue 4236 SER Chi-restraints excluded: chain B residue 4246 GLN Chi-restraints excluded: chain B residue 4338 VAL Chi-restraints excluded: chain B residue 4662 ASN Chi-restraints excluded: chain B residue 4704 LEU Chi-restraints excluded: chain B residue 4707 ASN Chi-restraints excluded: chain B residue 4778 TRP Chi-restraints excluded: chain B residue 4785 THR Chi-restraints excluded: chain B residue 5001 THR Chi-restraints excluded: chain C residue 4236 SER Chi-restraints excluded: chain C residue 4246 GLN Chi-restraints excluded: chain C residue 4338 VAL Chi-restraints excluded: chain C residue 4662 ASN Chi-restraints excluded: chain C residue 4704 LEU Chi-restraints excluded: chain C residue 4707 ASN Chi-restraints excluded: chain C residue 4778 TRP Chi-restraints excluded: chain C residue 4785 THR Chi-restraints excluded: chain C residue 5001 THR Chi-restraints excluded: chain D residue 4236 SER Chi-restraints excluded: chain D residue 4246 GLN Chi-restraints excluded: chain D residue 4338 VAL Chi-restraints excluded: chain D residue 4662 ASN Chi-restraints excluded: chain D residue 4704 LEU Chi-restraints excluded: chain D residue 4707 ASN Chi-restraints excluded: chain D residue 4778 TRP Chi-restraints excluded: chain D residue 4785 THR Chi-restraints excluded: chain D residue 5001 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4812 HIS B4812 HIS C4812 HIS D4812 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.185559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.157608 restraints weight = 17972.412| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 1.34 r_work: 0.3658 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16276 Z= 0.171 Angle : 0.564 8.499 22192 Z= 0.292 Chirality : 0.037 0.158 2488 Planarity : 0.004 0.037 2736 Dihedral : 6.778 61.157 2275 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.97 % Allowed : 22.74 % Favored : 73.29 % 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: 2.25 (0.19), residues: 2008 helix: 2.41 (0.13), residues: 1368 sheet: -0.47 (0.48), residues: 104 loop : -0.54 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C4192 TYR 0.014 0.002 TYR C4994 PHE 0.015 0.001 PHE C4916 TRP 0.011 0.001 TRP A4336 HIS 0.006 0.001 HIS D4803 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (16256) covalent geometry : angle 0.55244 / 0.29 (22180) SS BOND : bond 0.00064 / 0.03 ( 4) SS BOND : angle 0.69965 / 0.41 ( 8) hydrogen bonds : bond 0.04250 / 2.86 ( 1106) hydrogen bonds : angle 4.24808 / 3.16 ( 3222) metal coordination : bond 0.01148 / 0.68 ( 16) metal coordination : angle 8.49563 / 5.96 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 282 time to evaluate : 0.511 Fit side-chains REVERT: A 4218 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7822 (mp) REVERT: A 4778 TRP cc_start: 0.7416 (OUTLIER) cc_final: 0.6090 (t-100) REVERT: A 4879 MET cc_start: 0.8968 (mmm) cc_final: 0.8659 (tpt) REVERT: B 4218 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7810 (mp) REVERT: B 4778 TRP cc_start: 0.7412 (OUTLIER) cc_final: 0.6097 (t-100) REVERT: B 4879 MET cc_start: 0.8979 (mmm) cc_final: 0.8678 (tpt) REVERT: C 4218 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7831 (mp) REVERT: C 4778 TRP cc_start: 0.7403 (OUTLIER) cc_final: 0.6076 (t-100) REVERT: C 4879 MET cc_start: 0.8978 (mmm) cc_final: 0.8673 (tpt) REVERT: D 4778 TRP cc_start: 0.7411 (OUTLIER) cc_final: 0.6078 (t-100) REVERT: D 4879 MET cc_start: 0.8978 (mmm) cc_final: 0.8674 (tpt) outliers start: 58 outliers final: 19 residues processed: 313 average time/residue: 0.5253 time to fit residues: 184.4512 Evaluate side-chains 280 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 254 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4218 ILE Chi-restraints excluded: chain A residue 4631 PHE Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4707 ASN Chi-restraints excluded: chain A residue 4778 TRP Chi-restraints excluded: chain A residue 4958 CYS Chi-restraints excluded: chain B residue 4218 ILE Chi-restraints excluded: chain B residue 4338 VAL Chi-restraints excluded: chain B residue 4631 PHE Chi-restraints excluded: chain B residue 4704 LEU Chi-restraints excluded: chain B residue 4707 ASN Chi-restraints excluded: chain B residue 4778 TRP Chi-restraints excluded: chain B residue 4958 CYS Chi-restraints excluded: chain C residue 4218 ILE Chi-restraints excluded: chain C residue 4338 VAL Chi-restraints excluded: chain C residue 4631 PHE Chi-restraints excluded: chain C residue 4704 LEU Chi-restraints excluded: chain C residue 4707 ASN Chi-restraints excluded: chain C residue 4778 TRP Chi-restraints excluded: chain C residue 4958 CYS Chi-restraints excluded: chain D residue 4338 VAL Chi-restraints excluded: chain D residue 4631 PHE Chi-restraints excluded: chain D residue 4704 LEU Chi-restraints excluded: chain D residue 4707 ASN Chi-restraints excluded: chain D residue 4778 TRP Chi-restraints excluded: chain D residue 4958 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 25 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 174 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 136 optimal weight: 0.2980 chunk 172 optimal weight: 1.9990 chunk 201 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4250 GLN B4250 GLN C4250 GLN D4250 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.182863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.156175 restraints weight = 18184.168| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.38 r_work: 0.3608 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16276 Z= 0.155 Angle : 0.528 9.614 22192 Z= 0.273 Chirality : 0.036 0.183 2488 Planarity : 0.003 0.037 2736 Dihedral : 5.557 51.303 2243 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.73 % Allowed : 21.10 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.15 (0.18), residues: 2008 helix: 2.35 (0.13), residues: 1372 sheet: -0.70 (0.48), residues: 104 loop : -0.59 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C5017 TYR 0.014 0.001 TYR D4994 PHE 0.013 0.001 PHE B4916 TRP 0.006 0.001 TRP A4336 HIS 0.008 0.002 HIS D5003 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (16256) covalent geometry : angle 0.51178 / 0.27 (22180) SS BOND : bond 0.00116 / 0.06 ( 4) SS BOND : angle 0.66850 / 0.46 ( 8) hydrogen bonds : bond 0.04208 / 2.86 ( 1106) hydrogen bonds : angle 4.20238 / 3.12 ( 3222) metal coordination : bond 0.01162 / 0.68 ( 16) metal coordination : angle 9.60550 / 6.74 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 279 time to evaluate : 0.587 Fit side-chains REVERT: A 4218 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7789 (mp) REVERT: A 4562 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8386 (mm) REVERT: A 4778 TRP cc_start: 0.7400 (OUTLIER) cc_final: 0.6059 (t-100) REVERT: A 4879 MET cc_start: 0.8995 (mmm) cc_final: 0.8711 (tpt) REVERT: B 4218 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7791 (mp) REVERT: B 4562 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8374 (mm) REVERT: B 4778 TRP cc_start: 0.7400 (OUTLIER) cc_final: 0.6064 (t-100) REVERT: B 4879 MET cc_start: 0.9017 (mmm) cc_final: 0.8740 (tpt) REVERT: C 4218 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7810 (mp) REVERT: C 4562 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8385 (mm) REVERT: C 4778 TRP cc_start: 0.7399 (OUTLIER) cc_final: 0.6052 (t-100) REVERT: C 4879 MET cc_start: 0.9002 (mmm) cc_final: 0.8725 (tpt) REVERT: D 4562 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8377 (mm) REVERT: D 4778 TRP cc_start: 0.7404 (OUTLIER) cc_final: 0.6056 (t-100) REVERT: D 4879 MET cc_start: 0.9015 (mmm) cc_final: 0.8737 (tpt) outliers start: 69 outliers final: 22 residues processed: 329 average time/residue: 0.4901 time to fit residues: 181.9578 Evaluate side-chains 318 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 285 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4218 ILE Chi-restraints excluded: chain A residue 4562 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4631 PHE Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4707 ASN Chi-restraints excluded: chain A residue 4778 TRP Chi-restraints excluded: chain A residue 4958 CYS Chi-restraints excluded: chain B residue 4218 ILE Chi-restraints excluded: chain B residue 4338 VAL Chi-restraints excluded: chain B residue 4562 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4631 PHE Chi-restraints excluded: chain B residue 4704 LEU Chi-restraints excluded: chain B residue 4707 ASN Chi-restraints excluded: chain B residue 4778 TRP Chi-restraints excluded: chain B residue 4958 CYS Chi-restraints excluded: chain C residue 4218 ILE Chi-restraints excluded: chain C residue 4562 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4631 PHE Chi-restraints excluded: chain C residue 4704 LEU Chi-restraints excluded: chain C residue 4707 ASN Chi-restraints excluded: chain C residue 4778 TRP Chi-restraints excluded: chain C residue 4958 CYS Chi-restraints excluded: chain D residue 4338 VAL Chi-restraints excluded: chain D residue 4562 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4631 PHE Chi-restraints excluded: chain D residue 4704 LEU Chi-restraints excluded: chain D residue 4707 ASN Chi-restraints excluded: chain D residue 4778 TRP Chi-restraints excluded: chain D residue 4958 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 10 optimal weight: 4.9990 chunk 154 optimal weight: 0.8980 chunk 147 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 chunk 65 optimal weight: 0.0270 chunk 166 optimal weight: 0.4980 chunk 22 optimal weight: 0.0040 chunk 136 optimal weight: 0.1980 chunk 194 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.3050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4250 GLN B4250 GLN C4250 GLN D4250 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.184312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.158198 restraints weight = 17926.819| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.37 r_work: 0.3625 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16276 Z= 0.111 Angle : 0.491 8.041 22192 Z= 0.251 Chirality : 0.035 0.184 2488 Planarity : 0.003 0.037 2736 Dihedral : 5.468 51.655 2242 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.42 % Allowed : 23.84 % Favored : 72.74 % 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: 2.27 (0.19), residues: 2008 helix: 2.47 (0.13), residues: 1372 sheet: -0.89 (0.47), residues: 104 loop : -0.59 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C4192 TYR 0.012 0.001 TYR C5009 PHE 0.013 0.001 PHE C4237 TRP 0.006 0.001 TRP A4336 HIS 0.005 0.001 HIS D5003 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (16256) covalent geometry : angle 0.47871 / 0.25 (22180) SS BOND : bond 0.00020 / 0.01 ( 4) SS BOND : angle 0.39295 / 0.28 ( 8) hydrogen bonds : bond 0.03762 / 2.54 ( 1106) hydrogen bonds : angle 4.07655 / 3.04 ( 3222) metal coordination : bond 0.00859 / 0.51 ( 16) metal coordination : angle 8.03202 / 5.63 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 299 time to evaluate : 0.593 Fit side-chains REVERT: A 4192 ARG cc_start: 0.8179 (ttm110) cc_final: 0.7867 (ttm110) REVERT: A 4218 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7754 (mp) REVERT: A 4700 GLN cc_start: 0.8038 (mm-40) cc_final: 0.7701 (mm-40) REVERT: A 4778 TRP cc_start: 0.7391 (OUTLIER) cc_final: 0.6076 (t-100) REVERT: A 4879 MET cc_start: 0.8993 (mmm) cc_final: 0.8742 (tpt) REVERT: B 4192 ARG cc_start: 0.8169 (ttm110) cc_final: 0.7855 (ttm110) REVERT: B 4218 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7745 (mp) REVERT: B 4700 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7693 (mm-40) REVERT: B 4778 TRP cc_start: 0.7378 (OUTLIER) cc_final: 0.6076 (t-100) REVERT: B 4879 MET cc_start: 0.9002 (mmm) cc_final: 0.8755 (tpt) REVERT: C 4192 ARG cc_start: 0.8171 (ttm110) cc_final: 0.7861 (ttm110) REVERT: C 4218 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7761 (mp) REVERT: C 4700 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7694 (mm-40) REVERT: C 4778 TRP cc_start: 0.7384 (OUTLIER) cc_final: 0.6079 (t-100) REVERT: C 4879 MET cc_start: 0.9006 (mmm) cc_final: 0.8762 (tpt) REVERT: D 4192 ARG cc_start: 0.8180 (ttm110) cc_final: 0.7867 (ttm110) REVERT: D 4700 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7700 (mm-40) REVERT: D 4778 TRP cc_start: 0.7387 (OUTLIER) cc_final: 0.6070 (t-100) REVERT: D 4879 MET cc_start: 0.9007 (mmm) cc_final: 0.8761 (tpt) outliers start: 50 outliers final: 20 residues processed: 335 average time/residue: 0.4564 time to fit residues: 172.0047 Evaluate side-chains 308 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 281 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4218 ILE Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4631 PHE Chi-restraints excluded: chain A residue 4662 ASN Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4707 ASN Chi-restraints excluded: chain A residue 4778 TRP Chi-restraints excluded: chain B residue 4218 ILE Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4631 PHE Chi-restraints excluded: chain B residue 4662 ASN Chi-restraints excluded: chain B residue 4704 LEU Chi-restraints excluded: chain B residue 4707 ASN Chi-restraints excluded: chain B residue 4778 TRP Chi-restraints excluded: chain C residue 4218 ILE Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4631 PHE Chi-restraints excluded: chain C residue 4662 ASN Chi-restraints excluded: chain C residue 4704 LEU Chi-restraints excluded: chain C residue 4707 ASN Chi-restraints excluded: chain C residue 4778 TRP Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4631 PHE Chi-restraints excluded: chain D residue 4662 ASN Chi-restraints excluded: chain D residue 4704 LEU Chi-restraints excluded: chain D residue 4707 ASN Chi-restraints excluded: chain D residue 4778 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 178 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 136 optimal weight: 0.0870 chunk 83 optimal weight: 0.9990 chunk 103 optimal weight: 0.0070 chunk 56 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 60 optimal weight: 0.0980 chunk 3 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 105 optimal weight: 0.0980 overall best weight: 0.2576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4250 GLN B4250 GLN C4250 GLN D4250 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.184800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.158624 restraints weight = 18036.025| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.39 r_work: 0.3633 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16276 Z= 0.110 Angle : 0.485 7.858 22192 Z= 0.251 Chirality : 0.035 0.199 2488 Planarity : 0.003 0.035 2736 Dihedral : 5.342 51.067 2240 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.18 % Allowed : 23.63 % Favored : 72.19 % 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 (0.19), residues: 2008 helix: 2.46 (0.13), residues: 1372 sheet: -0.87 (0.48), residues: 104 loop : -0.52 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D4192 TYR 0.017 0.001 TYR A4630 PHE 0.012 0.001 PHE B4237 TRP 0.007 0.001 TRP B4716 HIS 0.004 0.001 HIS C5003 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (16256) covalent geometry : angle 0.47315 / 0.25 (22180) SS BOND : bond 0.00007 / 0.00 ( 4) SS BOND : angle 0.42227 / 0.30 ( 8) hydrogen bonds : bond 0.03696 / 2.49 ( 1106) hydrogen bonds : angle 4.02871 / 3.00 ( 3222) metal coordination : bond 0.00797 / 0.47 ( 16) metal coordination : angle 7.80446 / 5.45 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 316 time to evaluate : 0.476 Fit side-chains REVERT: A 4180 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7083 (mtm-85) REVERT: A 4214 LYS cc_start: 0.7796 (ttmt) cc_final: 0.7328 (ttpp) REVERT: A 4218 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7730 (mp) REVERT: A 4230 LYS cc_start: 0.8362 (ttpt) cc_final: 0.8136 (tttt) REVERT: A 4232 GLU cc_start: 0.6866 (mm-30) cc_final: 0.6338 (tm-30) REVERT: A 4562 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8322 (mm) REVERT: A 4700 GLN cc_start: 0.8018 (mm-40) cc_final: 0.7704 (mm-40) REVERT: A 4776 GLN cc_start: 0.6880 (mm-40) cc_final: 0.6384 (mm110) REVERT: A 4778 TRP cc_start: 0.7400 (OUTLIER) cc_final: 0.6036 (t-100) REVERT: A 4879 MET cc_start: 0.9003 (mmm) cc_final: 0.8692 (tpt) REVERT: B 4180 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.7087 (mtm-85) REVERT: B 4214 LYS cc_start: 0.7786 (ttmt) cc_final: 0.7312 (ttpp) REVERT: B 4218 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7726 (mp) REVERT: B 4230 LYS cc_start: 0.8368 (ttpt) cc_final: 0.8150 (tttt) REVERT: B 4232 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6335 (tm-30) REVERT: B 4562 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8311 (mm) REVERT: B 4700 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7692 (mm-40) REVERT: B 4776 GLN cc_start: 0.6901 (mm-40) cc_final: 0.6410 (mm110) REVERT: B 4778 TRP cc_start: 0.7392 (OUTLIER) cc_final: 0.6034 (t-100) REVERT: B 4879 MET cc_start: 0.9012 (mmm) cc_final: 0.8705 (tpt) REVERT: C 4180 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7060 (mtm-85) REVERT: C 4214 LYS cc_start: 0.7792 (ttmt) cc_final: 0.7319 (ttpp) REVERT: C 4218 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7740 (mp) REVERT: C 4230 LYS cc_start: 0.8370 (ttpt) cc_final: 0.8146 (tttt) REVERT: C 4232 GLU cc_start: 0.6854 (mm-30) cc_final: 0.6344 (tm-30) REVERT: C 4562 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8316 (mm) REVERT: C 4700 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7691 (mm-40) REVERT: C 4776 GLN cc_start: 0.6894 (mm-40) cc_final: 0.6397 (mm110) REVERT: C 4778 TRP cc_start: 0.7393 (OUTLIER) cc_final: 0.6033 (t-100) REVERT: C 4879 MET cc_start: 0.9007 (mmm) cc_final: 0.8704 (tpt) REVERT: D 4180 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7071 (mtm-85) REVERT: D 4230 LYS cc_start: 0.8365 (ttpt) cc_final: 0.8155 (tttt) REVERT: D 4232 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6318 (tm-30) REVERT: D 4562 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8305 (mm) REVERT: D 4700 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7695 (mm-40) REVERT: D 4776 GLN cc_start: 0.6889 (mm-40) cc_final: 0.6394 (mm110) REVERT: D 4778 TRP cc_start: 0.7396 (OUTLIER) cc_final: 0.6025 (t-100) REVERT: D 4879 MET cc_start: 0.9020 (mmm) cc_final: 0.8720 (tpt) outliers start: 61 outliers final: 24 residues processed: 360 average time/residue: 0.5573 time to fit residues: 222.7779 Evaluate side-chains 347 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 308 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4180 ARG Chi-restraints excluded: chain A residue 4218 ILE Chi-restraints excluded: chain A residue 4562 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4631 PHE Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4707 ASN Chi-restraints excluded: chain A residue 4778 TRP Chi-restraints excluded: chain A residue 4958 CYS Chi-restraints excluded: chain A residue 5014 TYR Chi-restraints excluded: chain B residue 4180 ARG Chi-restraints excluded: chain B residue 4218 ILE Chi-restraints excluded: chain B residue 4562 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4631 PHE Chi-restraints excluded: chain B residue 4704 LEU Chi-restraints excluded: chain B residue 4707 ASN Chi-restraints excluded: chain B residue 4778 TRP Chi-restraints excluded: chain B residue 4958 CYS Chi-restraints excluded: chain B residue 5014 TYR Chi-restraints excluded: chain C residue 4180 ARG Chi-restraints excluded: chain C residue 4218 ILE Chi-restraints excluded: chain C residue 4562 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4631 PHE Chi-restraints excluded: chain C residue 4704 LEU Chi-restraints excluded: chain C residue 4707 ASN Chi-restraints excluded: chain C residue 4778 TRP Chi-restraints excluded: chain C residue 4958 CYS Chi-restraints excluded: chain C residue 5014 TYR Chi-restraints excluded: chain D residue 4180 ARG Chi-restraints excluded: chain D residue 4562 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4631 PHE Chi-restraints excluded: chain D residue 4704 LEU Chi-restraints excluded: chain D residue 4707 ASN Chi-restraints excluded: chain D residue 4778 TRP Chi-restraints excluded: chain D residue 4937 ILE Chi-restraints excluded: chain D residue 4958 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 198 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 184 optimal weight: 0.8980 chunk 188 optimal weight: 0.4980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.178942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.152478 restraints weight = 17872.947| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.33 r_work: 0.3558 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16276 Z= 0.212 Angle : 0.601 11.041 22192 Z= 0.307 Chirality : 0.039 0.231 2488 Planarity : 0.004 0.040 2736 Dihedral : 5.473 51.464 2240 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.32 % Allowed : 24.11 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.18), residues: 2008 helix: 2.19 (0.13), residues: 1368 sheet: -0.93 (0.49), residues: 104 loop : -0.67 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C4192 TYR 0.014 0.002 TYR A4994 PHE 0.017 0.002 PHE D4916 TRP 0.008 0.002 TRP A4716 HIS 0.012 0.002 HIS D5003 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 (16256) covalent geometry : angle 0.58233 / 0.31 (22180) SS BOND : bond 0.00175 / 0.09 ( 4) SS BOND : angle 0.88760 / 0.62 ( 8) hydrogen bonds : bond 0.04411 / 2.98 ( 1106) hydrogen bonds : angle 4.30560 / 3.20 ( 3222) metal coordination : bond 0.01448 / 0.88 ( 16) metal coordination : angle 10.98618 / 7.68 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 271 time to evaluate : 0.625 Fit side-chains REVERT: A 4180 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7201 (mtm-85) REVERT: A 4232 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6562 (tm-30) REVERT: A 4562 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8396 (mm) REVERT: A 4700 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7775 (mm-40) REVERT: B 4180 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7214 (mtm-85) REVERT: B 4232 GLU cc_start: 0.6983 (mm-30) cc_final: 0.6562 (tm-30) REVERT: B 4562 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8404 (mm) REVERT: B 4700 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7772 (mm-40) REVERT: C 4180 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7183 (mtm-85) REVERT: C 4232 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6568 (tm-30) REVERT: C 4562 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8399 (mm) REVERT: C 4700 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7779 (mm-40) REVERT: D 4180 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7186 (mtm-85) REVERT: D 4218 ILE cc_start: 0.8044 (pt) cc_final: 0.7625 (mp) REVERT: D 4232 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6561 (tm-30) REVERT: D 4562 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8391 (mm) REVERT: D 4700 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7775 (mm-40) outliers start: 63 outliers final: 34 residues processed: 317 average time/residue: 0.5560 time to fit residues: 196.4579 Evaluate side-chains 317 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 275 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4178 LEU Chi-restraints excluded: chain A residue 4180 ARG Chi-restraints excluded: chain A residue 4562 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4631 PHE Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4707 ASN Chi-restraints excluded: chain A residue 4958 CYS Chi-restraints excluded: chain A residue 5014 TYR Chi-restraints excluded: chain B residue 4178 LEU Chi-restraints excluded: chain B residue 4180 ARG Chi-restraints excluded: chain B residue 4338 VAL Chi-restraints excluded: chain B residue 4562 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4631 PHE Chi-restraints excluded: chain B residue 4704 LEU Chi-restraints excluded: chain B residue 4707 ASN Chi-restraints excluded: chain B residue 4815 ASP Chi-restraints excluded: chain B residue 4839 MET Chi-restraints excluded: chain B residue 4958 CYS Chi-restraints excluded: chain B residue 5014 TYR Chi-restraints excluded: chain C residue 4178 LEU Chi-restraints excluded: chain C residue 4180 ARG Chi-restraints excluded: chain C residue 4562 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4631 PHE Chi-restraints excluded: chain C residue 4704 LEU Chi-restraints excluded: chain C residue 4707 ASN Chi-restraints excluded: chain C residue 4815 ASP Chi-restraints excluded: chain C residue 4958 CYS Chi-restraints excluded: chain C residue 5014 TYR Chi-restraints excluded: chain D residue 4178 LEU Chi-restraints excluded: chain D residue 4180 ARG Chi-restraints excluded: chain D residue 4338 VAL Chi-restraints excluded: chain D residue 4562 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4631 PHE Chi-restraints excluded: chain D residue 4704 LEU Chi-restraints excluded: chain D residue 4707 ASN Chi-restraints excluded: chain D residue 4815 ASP Chi-restraints excluded: chain D residue 4958 CYS Chi-restraints excluded: chain D residue 5014 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 177 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 192 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 200 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 202 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.178863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.151979 restraints weight = 17695.347| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.32 r_work: 0.3562 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16276 Z= 0.194 Angle : 0.592 10.799 22192 Z= 0.303 Chirality : 0.038 0.202 2488 Planarity : 0.004 0.041 2736 Dihedral : 5.260 52.012 2232 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.97 % Allowed : 25.34 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.18), residues: 2008 helix: 2.10 (0.13), residues: 1368 sheet: -0.95 (0.49), residues: 104 loop : -0.67 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C4192 TYR 0.014 0.002 TYR C4994 PHE 0.015 0.002 PHE B4916 TRP 0.009 0.001 TRP D4716 HIS 0.009 0.002 HIS A5003 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (16256) covalent geometry : angle 0.57406 / 0.30 (22180) SS BOND : bond 0.00238 / 0.12 ( 4) SS BOND : angle 0.77292 / 0.54 ( 8) hydrogen bonds : bond 0.04314 / 2.92 ( 1106) hydrogen bonds : angle 4.30032 / 3.19 ( 3222) metal coordination : bond 0.01392 / 0.82 ( 16) metal coordination : angle 10.76748 / 7.55 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 268 time to evaluate : 0.496 Fit side-chains REVERT: A 4180 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7064 (mtm-85) REVERT: A 4232 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6632 (tm-30) REVERT: A 4562 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8404 (mm) REVERT: A 4674 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7914 (tt0) REVERT: A 4700 GLN cc_start: 0.8064 (mm-40) cc_final: 0.7791 (mm-40) REVERT: A 4778 TRP cc_start: 0.7391 (OUTLIER) cc_final: 0.5895 (t-100) REVERT: A 4879 MET cc_start: 0.9011 (mmm) cc_final: 0.8771 (tpt) REVERT: B 4180 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7091 (mtm-85) REVERT: B 4232 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6631 (tm-30) REVERT: B 4562 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8412 (mm) REVERT: B 4674 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7912 (tt0) REVERT: B 4700 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7787 (mm-40) REVERT: B 4778 TRP cc_start: 0.7389 (OUTLIER) cc_final: 0.5895 (t-100) REVERT: B 4879 MET cc_start: 0.9033 (mmm) cc_final: 0.8795 (tpt) REVERT: C 4180 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7066 (mtm-85) REVERT: C 4232 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6638 (tm-30) REVERT: C 4562 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8404 (mm) REVERT: C 4700 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7802 (mm-40) REVERT: C 4778 TRP cc_start: 0.7392 (OUTLIER) cc_final: 0.5878 (t-100) REVERT: C 4879 MET cc_start: 0.9013 (mmm) cc_final: 0.8777 (tpt) REVERT: D 4180 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7056 (mtm-85) REVERT: D 4232 GLU cc_start: 0.7040 (mm-30) cc_final: 0.6619 (tm-30) REVERT: D 4562 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8406 (mm) REVERT: D 4700 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7806 (mm-40) REVERT: D 4778 TRP cc_start: 0.7397 (OUTLIER) cc_final: 0.5880 (t-100) REVERT: D 4879 MET cc_start: 0.9022 (mmm) cc_final: 0.8783 (tpt) outliers start: 58 outliers final: 33 residues processed: 310 average time/residue: 0.5177 time to fit residues: 179.7574 Evaluate side-chains 313 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 266 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4178 LEU Chi-restraints excluded: chain A residue 4180 ARG Chi-restraints excluded: chain A residue 4562 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4631 PHE Chi-restraints excluded: chain A residue 4662 ASN Chi-restraints excluded: chain A residue 4674 GLU Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4707 ASN Chi-restraints excluded: chain A residue 4778 TRP Chi-restraints excluded: chain A residue 4958 CYS Chi-restraints excluded: chain A residue 5014 TYR Chi-restraints excluded: chain B residue 4178 LEU Chi-restraints excluded: chain B residue 4180 ARG Chi-restraints excluded: chain B residue 4562 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4631 PHE Chi-restraints excluded: chain B residue 4662 ASN Chi-restraints excluded: chain B residue 4674 GLU Chi-restraints excluded: chain B residue 4704 LEU Chi-restraints excluded: chain B residue 4707 ASN Chi-restraints excluded: chain B residue 4778 TRP Chi-restraints excluded: chain B residue 4839 MET Chi-restraints excluded: chain B residue 4958 CYS Chi-restraints excluded: chain B residue 5014 TYR Chi-restraints excluded: chain C residue 4178 LEU Chi-restraints excluded: chain C residue 4180 ARG Chi-restraints excluded: chain C residue 4562 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4631 PHE Chi-restraints excluded: chain C residue 4662 ASN Chi-restraints excluded: chain C residue 4704 LEU Chi-restraints excluded: chain C residue 4707 ASN Chi-restraints excluded: chain C residue 4778 TRP Chi-restraints excluded: chain C residue 4958 CYS Chi-restraints excluded: chain C residue 5014 TYR Chi-restraints excluded: chain D residue 4178 LEU Chi-restraints excluded: chain D residue 4180 ARG Chi-restraints excluded: chain D residue 4562 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4631 PHE Chi-restraints excluded: chain D residue 4662 ASN Chi-restraints excluded: chain D residue 4704 LEU Chi-restraints excluded: chain D residue 4707 ASN Chi-restraints excluded: chain D residue 4778 TRP Chi-restraints excluded: chain D residue 4958 CYS Chi-restraints excluded: chain D residue 5014 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 58 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 14 optimal weight: 0.0470 chunk 142 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.179745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.152280 restraints weight = 17935.884| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.38 r_work: 0.3566 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16276 Z= 0.163 Angle : 0.572 9.932 22192 Z= 0.294 Chirality : 0.037 0.245 2488 Planarity : 0.004 0.045 2736 Dihedral : 5.208 52.334 2232 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.70 % Allowed : 25.62 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.18), residues: 2008 helix: 2.09 (0.13), residues: 1368 sheet: -1.11 (0.48), residues: 104 loop : -0.63 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D4192 TYR 0.022 0.001 TYR A4630 PHE 0.017 0.001 PHE A4237 TRP 0.008 0.001 TRP D4716 HIS 0.007 0.001 HIS C5003 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (16256) covalent geometry : angle 0.55670 / 0.29 (22180) SS BOND : bond 0.00187 / 0.09 ( 4) SS BOND : angle 0.66317 / 0.46 ( 8) hydrogen bonds : bond 0.04163 / 2.82 ( 1106) hydrogen bonds : angle 4.28012 / 3.18 ( 3222) metal coordination : bond 0.01198 / 0.70 ( 16) metal coordination : angle 9.91014 / 6.95 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 281 time to evaluate : 0.539 Fit side-chains REVERT: A 4180 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7097 (mtm-85) REVERT: A 4192 ARG cc_start: 0.8161 (ttm110) cc_final: 0.7948 (ttm110) REVERT: A 4232 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6635 (tm-30) REVERT: A 4700 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7805 (mm-40) REVERT: A 4879 MET cc_start: 0.8999 (mmm) cc_final: 0.8767 (tpt) REVERT: B 4180 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7109 (mtm-85) REVERT: B 4192 ARG cc_start: 0.8164 (ttm110) cc_final: 0.7948 (ttm110) REVERT: B 4232 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6635 (tm-30) REVERT: B 4700 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7807 (mm-40) REVERT: B 4879 MET cc_start: 0.9031 (mmm) cc_final: 0.8803 (tpt) REVERT: C 4180 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7100 (mtm-85) REVERT: C 4192 ARG cc_start: 0.8156 (ttm110) cc_final: 0.7938 (ttm110) REVERT: C 4232 GLU cc_start: 0.7101 (mm-30) cc_final: 0.6643 (tm-30) REVERT: C 4700 GLN cc_start: 0.8065 (mm-40) cc_final: 0.7809 (mm-40) REVERT: C 4879 MET cc_start: 0.8996 (mmm) cc_final: 0.8771 (tpt) REVERT: D 4180 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7064 (mtm-85) REVERT: D 4192 ARG cc_start: 0.8173 (ttm110) cc_final: 0.7951 (ttm110) REVERT: D 4218 ILE cc_start: 0.8156 (pt) cc_final: 0.7713 (mp) REVERT: D 4232 GLU cc_start: 0.7105 (mm-30) cc_final: 0.6653 (tm-30) REVERT: D 4237 PHE cc_start: 0.8554 (t80) cc_final: 0.8320 (t80) REVERT: D 4700 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7819 (mm-40) REVERT: D 4879 MET cc_start: 0.9015 (mmm) cc_final: 0.8781 (tpt) outliers start: 54 outliers final: 33 residues processed: 323 average time/residue: 0.4553 time to fit residues: 165.8204 Evaluate side-chains 308 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 271 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4178 LEU Chi-restraints excluded: chain A residue 4180 ARG Chi-restraints excluded: chain A residue 4218 ILE Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4631 PHE Chi-restraints excluded: chain A residue 4662 ASN Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4958 CYS Chi-restraints excluded: chain A residue 5014 TYR Chi-restraints excluded: chain B residue 4178 LEU Chi-restraints excluded: chain B residue 4180 ARG Chi-restraints excluded: chain B residue 4218 ILE Chi-restraints excluded: chain B residue 4338 VAL Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4631 PHE Chi-restraints excluded: chain B residue 4662 ASN Chi-restraints excluded: chain B residue 4704 LEU Chi-restraints excluded: chain B residue 4958 CYS Chi-restraints excluded: chain B residue 5014 TYR Chi-restraints excluded: chain C residue 4178 LEU Chi-restraints excluded: chain C residue 4180 ARG Chi-restraints excluded: chain C residue 4218 ILE Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4631 PHE Chi-restraints excluded: chain C residue 4662 ASN Chi-restraints excluded: chain C residue 4704 LEU Chi-restraints excluded: chain C residue 4958 CYS Chi-restraints excluded: chain C residue 5014 TYR Chi-restraints excluded: chain D residue 4178 LEU Chi-restraints excluded: chain D residue 4180 ARG Chi-restraints excluded: chain D residue 4338 VAL Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4631 PHE Chi-restraints excluded: chain D residue 4662 ASN Chi-restraints excluded: chain D residue 4704 LEU Chi-restraints excluded: chain D residue 4958 CYS Chi-restraints excluded: chain D residue 5014 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 187 optimal weight: 0.2980 chunk 53 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 88 optimal weight: 0.1980 chunk 202 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 183 optimal weight: 0.0770 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.181971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.154636 restraints weight = 17868.077| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.39 r_work: 0.3595 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16276 Z= 0.127 Angle : 0.563 8.857 22192 Z= 0.289 Chirality : 0.036 0.231 2488 Planarity : 0.004 0.043 2736 Dihedral : 5.000 51.863 2224 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.15 % Allowed : 26.44 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.18), residues: 2008 helix: 2.16 (0.13), residues: 1368 sheet: -1.10 (0.49), residues: 104 loop : -0.57 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B4192 TYR 0.020 0.001 TYR B4630 PHE 0.020 0.001 PHE B4237 TRP 0.008 0.001 TRP D4716 HIS 0.004 0.001 HIS D5003 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (16256) covalent geometry : angle 0.55016 / 0.29 (22180) SS BOND : bond 0.00037 / 0.02 ( 4) SS BOND : angle 0.53402 / 0.38 ( 8) hydrogen bonds : bond 0.03935 / 2.66 ( 1106) hydrogen bonds : angle 4.22500 / 3.14 ( 3222) metal coordination : bond 0.00952 / 0.55 ( 16) metal coordination : angle 8.81972 / 6.17 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 288 time to evaluate : 0.649 Fit side-chains REVERT: A 4180 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7016 (mtm-85) REVERT: A 4192 ARG cc_start: 0.8131 (ttm110) cc_final: 0.7918 (ttm110) REVERT: A 4232 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6540 (tm-30) REVERT: A 4631 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.7277 (m-80) REVERT: A 4700 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7786 (mm-40) REVERT: A 4879 MET cc_start: 0.9020 (mmm) cc_final: 0.8754 (tpt) REVERT: B 4180 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7047 (mtm-85) REVERT: B 4192 ARG cc_start: 0.8126 (ttm110) cc_final: 0.7912 (ttm110) REVERT: B 4232 GLU cc_start: 0.6998 (mm-30) cc_final: 0.6538 (tm-30) REVERT: B 4700 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7770 (mm-40) REVERT: B 4879 MET cc_start: 0.9039 (mmm) cc_final: 0.8793 (tpt) REVERT: C 4180 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7038 (mtm-85) REVERT: C 4192 ARG cc_start: 0.8127 (ttm110) cc_final: 0.7915 (ttm110) REVERT: C 4232 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6569 (tm-30) REVERT: C 4649 LEU cc_start: 0.8115 (mm) cc_final: 0.7899 (mp) REVERT: C 4700 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7779 (mm-40) REVERT: C 4879 MET cc_start: 0.9031 (mmm) cc_final: 0.8772 (tpt) REVERT: D 4180 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7026 (mtm-85) REVERT: D 4192 ARG cc_start: 0.8145 (ttm110) cc_final: 0.7934 (ttm110) REVERT: D 4232 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6593 (tm-30) REVERT: D 4700 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7792 (mm-40) REVERT: D 4879 MET cc_start: 0.9028 (mmm) cc_final: 0.8781 (tpt) outliers start: 46 outliers final: 32 residues processed: 321 average time/residue: 0.4857 time to fit residues: 175.5409 Evaluate side-chains 315 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 278 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4178 LEU Chi-restraints excluded: chain A residue 4180 ARG Chi-restraints excluded: chain A residue 4218 ILE Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4631 PHE Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4958 CYS Chi-restraints excluded: chain A residue 5014 TYR Chi-restraints excluded: chain B residue 4178 LEU Chi-restraints excluded: chain B residue 4180 ARG Chi-restraints excluded: chain B residue 4218 ILE Chi-restraints excluded: chain B residue 4338 VAL Chi-restraints excluded: chain B residue 4562 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4631 PHE Chi-restraints excluded: chain B residue 4704 LEU Chi-restraints excluded: chain B residue 4839 MET Chi-restraints excluded: chain B residue 4958 CYS Chi-restraints excluded: chain B residue 5014 TYR Chi-restraints excluded: chain C residue 4178 LEU Chi-restraints excluded: chain C residue 4180 ARG Chi-restraints excluded: chain C residue 4218 ILE Chi-restraints excluded: chain C residue 4562 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4631 PHE Chi-restraints excluded: chain C residue 4704 LEU Chi-restraints excluded: chain C residue 4958 CYS Chi-restraints excluded: chain C residue 5014 TYR Chi-restraints excluded: chain D residue 4178 LEU Chi-restraints excluded: chain D residue 4180 ARG Chi-restraints excluded: chain D residue 4338 VAL Chi-restraints excluded: chain D residue 4562 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4631 PHE Chi-restraints excluded: chain D residue 4704 LEU Chi-restraints excluded: chain D residue 4958 CYS Chi-restraints excluded: chain D residue 5014 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 155 optimal weight: 0.6980 chunk 171 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 201 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.179016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.150878 restraints weight = 17731.971| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.44 r_work: 0.3541 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16276 Z= 0.191 Angle : 0.614 10.721 22192 Z= 0.313 Chirality : 0.038 0.256 2488 Planarity : 0.004 0.041 2736 Dihedral : 5.104 52.662 2224 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.95 % Allowed : 26.30 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.19), residues: 2008 helix: 1.98 (0.13), residues: 1384 sheet: -1.17 (0.48), residues: 104 loop : -0.56 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B4192 TYR 0.018 0.002 TYR C4630 PHE 0.018 0.002 PHE D4237 TRP 0.009 0.001 TRP D4716 HIS 0.010 0.002 HIS D5003 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (16256) covalent geometry : angle 0.59665 / 0.31 (22180) SS BOND : bond 0.00239 / 0.12 ( 4) SS BOND : angle 0.70147 / 0.47 ( 8) hydrogen bonds : bond 0.04291 / 2.89 ( 1106) hydrogen bonds : angle 4.35819 / 3.23 ( 3222) metal coordination : bond 0.01311 / 0.76 ( 16) metal coordination : angle 10.68863 / 7.49 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 271 time to evaluate : 0.563 Fit side-chains REVERT: A 4180 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7051 (mtm-85) REVERT: A 4192 ARG cc_start: 0.8168 (ttm110) cc_final: 0.7950 (ttm110) REVERT: A 4232 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6628 (tm-30) REVERT: A 4631 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.7485 (m-80) REVERT: A 4700 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7822 (mm-40) REVERT: A 4784 PHE cc_start: 0.8544 (m-80) cc_final: 0.8330 (m-80) REVERT: A 4879 MET cc_start: 0.8992 (mmm) cc_final: 0.8744 (tpt) REVERT: B 4180 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7068 (mtm-85) REVERT: B 4192 ARG cc_start: 0.8159 (ttm110) cc_final: 0.7939 (ttm110) REVERT: B 4232 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6651 (tm-30) REVERT: B 4700 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7819 (mm-40) REVERT: B 4784 PHE cc_start: 0.8516 (m-80) cc_final: 0.8309 (m-80) REVERT: B 4879 MET cc_start: 0.9015 (mmm) cc_final: 0.8765 (tpt) REVERT: C 4180 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7077 (mtm-85) REVERT: C 4192 ARG cc_start: 0.8158 (ttm110) cc_final: 0.7929 (ttm110) REVERT: C 4232 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6647 (tm-30) REVERT: C 4700 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7801 (mm-40) REVERT: C 4784 PHE cc_start: 0.8505 (m-80) cc_final: 0.8298 (m-80) REVERT: C 4879 MET cc_start: 0.8984 (mmm) cc_final: 0.8740 (tpt) REVERT: D 4180 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7058 (mtm-85) REVERT: D 4192 ARG cc_start: 0.8164 (ttm110) cc_final: 0.7929 (ttm110) REVERT: D 4218 ILE cc_start: 0.8171 (pt) cc_final: 0.7727 (mp) REVERT: D 4232 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6659 (tm-30) REVERT: D 4237 PHE cc_start: 0.8533 (t80) cc_final: 0.8311 (t80) REVERT: D 4700 GLN cc_start: 0.8080 (mm-40) cc_final: 0.7824 (mm-40) REVERT: D 4784 PHE cc_start: 0.8543 (m-80) cc_final: 0.8330 (m-80) REVERT: D 4879 MET cc_start: 0.9018 (mmm) cc_final: 0.8776 (tpt) outliers start: 43 outliers final: 32 residues processed: 301 average time/residue: 0.5194 time to fit residues: 175.3281 Evaluate side-chains 307 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 270 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4178 LEU Chi-restraints excluded: chain A residue 4180 ARG Chi-restraints excluded: chain A residue 4218 ILE Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4631 PHE Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4958 CYS Chi-restraints excluded: chain A residue 5014 TYR Chi-restraints excluded: chain B residue 4178 LEU Chi-restraints excluded: chain B residue 4180 ARG Chi-restraints excluded: chain B residue 4218 ILE Chi-restraints excluded: chain B residue 4338 VAL Chi-restraints excluded: chain B residue 4562 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4631 PHE Chi-restraints excluded: chain B residue 4704 LEU Chi-restraints excluded: chain B residue 4839 MET Chi-restraints excluded: chain B residue 4958 CYS Chi-restraints excluded: chain B residue 5014 TYR Chi-restraints excluded: chain C residue 4178 LEU Chi-restraints excluded: chain C residue 4180 ARG Chi-restraints excluded: chain C residue 4218 ILE Chi-restraints excluded: chain C residue 4562 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4631 PHE Chi-restraints excluded: chain C residue 4704 LEU Chi-restraints excluded: chain C residue 4958 CYS Chi-restraints excluded: chain C residue 5014 TYR Chi-restraints excluded: chain D residue 4178 LEU Chi-restraints excluded: chain D residue 4180 ARG Chi-restraints excluded: chain D residue 4338 VAL Chi-restraints excluded: chain D residue 4562 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4631 PHE Chi-restraints excluded: chain D residue 4704 LEU Chi-restraints excluded: chain D residue 4958 CYS Chi-restraints excluded: chain D residue 5014 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 139 optimal weight: 0.0060 chunk 149 optimal weight: 0.7980 chunk 182 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 142 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 52 optimal weight: 0.0980 chunk 140 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.181078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.153663 restraints weight = 17817.812| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.37 r_work: 0.3588 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16276 Z= 0.129 Angle : 0.566 8.799 22192 Z= 0.291 Chirality : 0.037 0.244 2488 Planarity : 0.004 0.039 2736 Dihedral : 5.021 52.354 2224 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.81 % Allowed : 27.12 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.19), residues: 2008 helix: 2.09 (0.13), residues: 1384 sheet: -1.17 (0.49), residues: 104 loop : -0.45 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B4192 TYR 0.018 0.001 TYR C4630 PHE 0.020 0.001 PHE D4237 TRP 0.009 0.001 TRP C4205 HIS 0.005 0.001 HIS C5003 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (16256) covalent geometry : angle 0.55334 / 0.29 (22180) SS BOND : bond 0.00029 / 0.02 ( 4) SS BOND : angle 0.54368 / 0.38 ( 8) hydrogen bonds : bond 0.03949 / 2.66 ( 1106) hydrogen bonds : angle 4.26578 / 3.16 ( 3222) metal coordination : bond 0.00977 / 0.56 ( 16) metal coordination : angle 8.76915 / 6.14 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6203.00 seconds wall clock time: 106 minutes 23.06 seconds (6383.06 seconds total)