Starting phenix.real_space_refine on Sat Jun 14 12:34:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8drp_27680/06_2025/8drp_27680.cif Found real_map, /net/cci-nas-00/data/ceres_data/8drp_27680/06_2025/8drp_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8drp_27680/06_2025/8drp_27680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8drp_27680/06_2025/8drp_27680.map" model { file = "/net/cci-nas-00/data/ceres_data/8drp_27680/06_2025/8drp_27680.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8drp_27680/06_2025/8drp_27680.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 3, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 18, 'GLU:plan': 31, 'ARG:plan': 6} 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: {'GLN:plan1': 3, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 18, 'GLU:plan': 31, 'ARG:plan': 6} 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: {'GLN:plan1': 3, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 18, 'GLU:plan': 31, 'ARG:plan': 6} 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: {'GLN:plan1': 3, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 18, 'GLU:plan': 31, 'ARG:plan': 6} 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: 10.65, per 1000 atoms: 0.67 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: 4.17 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.57 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: 5.41 Time building geometry restraints manager: 4.85 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 - 16.28: 7864 16.28 - 32.56: 853 32.56 - 48.84: 423 48.84 - 65.11: 80 65.11 - 81.39: 28 Dihedral angle restraints: 9248 sinusoidal: 3244 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 9245 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 6.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 42.060 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 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 : 17.638 81.393 5372 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (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 TRP 0.011 0.001 TRP B4716 HIS 0.001 0.000 HIS B4978 PHE 0.011 0.001 PHE D4711 TYR 0.018 0.001 TYR C5014 ARG 0.007 0.001 ARG A5029 Details of bonding type rmsd hydrogen bonds : bond 0.14263 ( 1106) hydrogen bonds : angle 5.00027 ( 3222) metal coordination : bond 0.00607 ( 16) metal coordination : angle 6.13153 ( 4) SS BOND : bond 0.01820 ( 4) SS BOND : angle 1.42130 ( 8) covalent geometry : bond 0.00414 (16256) covalent geometry : angle 0.70621 (22180) *********************** 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 : 1.643 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: 1.3281 time to fit residues: 500.7465 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 : 1.901 ------------------------------------------------------------------------------- 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 172 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3997 r_free = 0.3997 target = 0.181383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.152940 restraints weight = 17872.012| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.34 r_work: 0.3593 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16276 Z= 0.233 Angle : 0.617 10.193 22192 Z= 0.321 Chirality : 0.040 0.165 2488 Planarity : 0.004 0.037 2736 Dihedral : 10.313 89.667 2399 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.25 % Allowed : 22.33 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.18), residues: 2008 helix: 2.24 (0.13), residues: 1364 sheet: -0.63 (0.47), residues: 104 loop : -0.67 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A4336 HIS 0.010 0.002 HIS D5003 PHE 0.020 0.002 PHE A4916 TYR 0.019 0.002 TYR D4994 ARG 0.007 0.001 ARG A4192 Details of bonding type rmsd hydrogen bonds : bond 0.04674 ( 1106) hydrogen bonds : angle 4.38634 ( 3222) metal coordination : bond 0.01677 ( 16) metal coordination : angle 10.18968 ( 4) SS BOND : bond 0.00341 ( 4) SS BOND : angle 0.74037 ( 8) covalent geometry : bond 0.00528 (16256) covalent geometry : angle 0.60192 (22180) *********************** 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 372 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 310 time to evaluate : 2.069 Fit side-chains REVERT: A 4700 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7730 (mm-40) REVERT: A 4778 TRP cc_start: 0.7443 (OUTLIER) cc_final: 0.6098 (t-100) REVERT: A 4948 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: B 4700 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7729 (mm-40) REVERT: B 4778 TRP cc_start: 0.7441 (OUTLIER) cc_final: 0.6106 (t-100) REVERT: B 4948 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: C 4700 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7724 (mm-40) REVERT: C 4778 TRP cc_start: 0.7435 (OUTLIER) cc_final: 0.6090 (t-100) REVERT: C 4948 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: D 4700 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7723 (mm-40) REVERT: D 4778 TRP cc_start: 0.7445 (OUTLIER) cc_final: 0.6095 (t-100) REVERT: D 4948 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7195 (mp0) outliers start: 62 outliers final: 19 residues processed: 341 average time/residue: 1.3039 time to fit residues: 496.4921 Evaluate side-chains 305 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 278 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 4948 GLU Chi-restraints excluded: chain A residue 4958 CYS 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 4948 GLU Chi-restraints excluded: chain B residue 4958 CYS 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 4948 GLU 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 4948 GLU 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 197 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 chunk 191 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 190 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 201 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3981 r_free = 0.3981 target = 0.179775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.152744 restraints weight = 17914.928| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.37 r_work: 0.3570 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16276 Z= 0.175 Angle : 0.545 10.496 22192 Z= 0.283 Chirality : 0.037 0.185 2488 Planarity : 0.004 0.040 2736 Dihedral : 9.634 85.207 2367 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.79 % Allowed : 21.85 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.18), residues: 2008 helix: 2.22 (0.13), residues: 1368 sheet: -0.69 (0.48), residues: 104 loop : -0.76 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A4336 HIS 0.008 0.002 HIS C5003 PHE 0.013 0.001 PHE D4916 TYR 0.015 0.002 TYR A4994 ARG 0.009 0.001 ARG D4192 Details of bonding type rmsd hydrogen bonds : bond 0.04343 ( 1106) hydrogen bonds : angle 4.25338 ( 3222) metal coordination : bond 0.01343 ( 16) metal coordination : angle 10.48873 ( 4) SS BOND : bond 0.00051 ( 4) SS BOND : angle 0.77807 ( 8) covalent geometry : bond 0.00391 (16256) covalent geometry : angle 0.52610 (22180) *********************** 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 345 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 275 time to evaluate : 3.044 Fit side-chains REVERT: A 4232 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6397 (tm-30) REVERT: A 4549 VAL cc_start: 0.6779 (m) cc_final: 0.6514 (p) REVERT: A 4562 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8414 (mm) REVERT: A 4776 GLN cc_start: 0.7037 (mm-40) cc_final: 0.6728 (mm-40) REVERT: A 4778 TRP cc_start: 0.7378 (OUTLIER) cc_final: 0.6025 (t-100) REVERT: A 4879 MET cc_start: 0.8991 (mmm) cc_final: 0.8734 (tpt) REVERT: B 4232 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6381 (tm-30) REVERT: B 4549 VAL cc_start: 0.6790 (m) cc_final: 0.6539 (p) REVERT: B 4562 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8419 (mm) REVERT: B 4776 GLN cc_start: 0.7039 (mm-40) cc_final: 0.6734 (mm-40) REVERT: B 4778 TRP cc_start: 0.7378 (OUTLIER) cc_final: 0.6027 (t-100) REVERT: B 4879 MET cc_start: 0.9034 (mmm) cc_final: 0.8785 (tpt) REVERT: C 4232 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6393 (tm-30) REVERT: C 4549 VAL cc_start: 0.6800 (m) cc_final: 0.6536 (p) REVERT: C 4562 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8424 (mm) REVERT: C 4776 GLN cc_start: 0.7028 (mm-40) cc_final: 0.6721 (mm-40) REVERT: C 4778 TRP cc_start: 0.7376 (OUTLIER) cc_final: 0.6014 (t-100) REVERT: C 4879 MET cc_start: 0.9006 (mmm) cc_final: 0.8759 (tpt) REVERT: C 4948 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7261 (mp0) REVERT: D 4232 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6374 (tm-30) REVERT: D 4549 VAL cc_start: 0.6789 (m) cc_final: 0.6527 (p) REVERT: D 4562 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8424 (mm) REVERT: D 4776 GLN cc_start: 0.7026 (mm-40) cc_final: 0.6715 (mm-40) REVERT: D 4778 TRP cc_start: 0.7380 (OUTLIER) cc_final: 0.6018 (t-100) REVERT: D 4879 MET cc_start: 0.9008 (mmm) cc_final: 0.8757 (tpt) REVERT: D 4948 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7247 (mp0) outliers start: 70 outliers final: 22 residues processed: 325 average time/residue: 1.3394 time to fit residues: 489.5689 Evaluate side-chains 293 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 261 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 4948 GLU 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 4948 GLU 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 32 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 175 optimal weight: 0.0040 chunk 22 optimal weight: 0.0670 chunk 134 optimal weight: 0.9990 chunk 196 optimal weight: 0.0770 chunk 90 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 200 optimal weight: 0.1980 overall best weight: 0.2088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4022 r_free = 0.4022 target = 0.183453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.157357 restraints weight = 18021.999| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 1.39 r_work: 0.3626 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2224 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= 0.107 Angle : 0.505 8.043 22192 Z= 0.257 Chirality : 0.035 0.185 2488 Planarity : 0.003 0.038 2736 Dihedral : 9.461 88.816 2366 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.97 % Allowed : 22.81 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.18), residues: 2008 helix: 2.45 (0.13), residues: 1348 sheet: -0.75 (0.48), residues: 104 loop : -0.51 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C4716 HIS 0.004 0.001 HIS A5003 PHE 0.014 0.001 PHE D4237 TYR 0.014 0.001 TYR D4994 ARG 0.010 0.001 ARG A4192 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 1106) hydrogen bonds : angle 4.05386 ( 3222) metal coordination : bond 0.00830 ( 16) metal coordination : angle 8.02497 ( 4) SS BOND : bond 0.00017 ( 4) SS BOND : angle 0.35131 ( 8) covalent geometry : bond 0.00222 (16256) covalent geometry : angle 0.49304 (22180) *********************** 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 348 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 290 time to evaluate : 1.760 Fit side-chains REVERT: A 4218 ILE cc_start: 0.8191 (mm) cc_final: 0.7932 (mp) REVERT: A 4232 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6346 (tm-30) REVERT: A 4700 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7687 (mm-40) REVERT: A 4778 TRP cc_start: 0.7400 (OUTLIER) cc_final: 0.6126 (t-100) REVERT: A 4879 MET cc_start: 0.9022 (mmm) cc_final: 0.8773 (tpt) REVERT: B 4218 ILE cc_start: 0.8185 (mm) cc_final: 0.7925 (mp) REVERT: B 4232 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6353 (tm-30) REVERT: B 4700 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7677 (mm-40) REVERT: B 4778 TRP cc_start: 0.7394 (OUTLIER) cc_final: 0.6125 (t-100) REVERT: B 4879 MET cc_start: 0.9049 (mmm) cc_final: 0.8806 (tpt) REVERT: C 4218 ILE cc_start: 0.8194 (mm) cc_final: 0.7934 (mp) REVERT: C 4232 GLU cc_start: 0.6944 (mm-30) cc_final: 0.6332 (tm-30) REVERT: C 4700 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7687 (mm-40) REVERT: C 4778 TRP cc_start: 0.7394 (OUTLIER) cc_final: 0.6117 (t-100) REVERT: C 4879 MET cc_start: 0.9034 (mmm) cc_final: 0.8791 (tpt) REVERT: D 4232 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6335 (tm-30) REVERT: D 4700 GLN cc_start: 0.8018 (mm-40) cc_final: 0.7692 (mm-40) REVERT: D 4778 TRP cc_start: 0.7401 (OUTLIER) cc_final: 0.6111 (t-100) REVERT: D 4879 MET cc_start: 0.9040 (mmm) cc_final: 0.8801 (tpt) outliers start: 58 outliers final: 20 residues processed: 330 average time/residue: 1.1513 time to fit residues: 423.3131 Evaluate side-chains 298 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 274 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 117 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 73 optimal weight: 0.0020 chunk 165 optimal weight: 2.9990 chunk 202 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 179 optimal weight: 0.7980 chunk 160 optimal weight: 0.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.180773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.154361 restraints weight = 18159.579| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.38 r_work: 0.3572 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16276 Z= 0.158 Angle : 0.541 10.059 22192 Z= 0.278 Chirality : 0.037 0.213 2488 Planarity : 0.003 0.040 2736 Dihedral : 9.346 87.014 2364 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.93 % Allowed : 22.40 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.18), residues: 2008 helix: 2.40 (0.13), residues: 1348 sheet: -0.73 (0.49), residues: 104 loop : -0.52 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A4716 HIS 0.008 0.001 HIS D5003 PHE 0.014 0.001 PHE B4916 TYR 0.014 0.001 TYR B4994 ARG 0.010 0.001 ARG D4192 Details of bonding type rmsd hydrogen bonds : bond 0.04079 ( 1106) hydrogen bonds : angle 4.15382 ( 3222) metal coordination : bond 0.01183 ( 16) metal coordination : angle 10.04513 ( 4) SS BOND : bond 0.00102 ( 4) SS BOND : angle 0.63869 ( 8) covalent geometry : bond 0.00357 (16256) covalent geometry : angle 0.52392 (22180) *********************** 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 358 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 286 time to evaluate : 1.698 Fit side-chains REVERT: A 4180 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7203 (mtm-85) REVERT: A 4232 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6429 (tm-30) REVERT: A 4549 VAL cc_start: 0.6607 (m) cc_final: 0.6368 (p) REVERT: A 4562 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8347 (mm) REVERT: A 4700 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7677 (mm-40) REVERT: A 4778 TRP cc_start: 0.7340 (OUTLIER) cc_final: 0.5936 (t-100) REVERT: A 4879 MET cc_start: 0.9049 (mmm) cc_final: 0.8785 (tpt) REVERT: A 5031 GLN cc_start: 0.6547 (OUTLIER) cc_final: 0.6346 (tt0) REVERT: B 4180 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7217 (mtm-85) REVERT: B 4232 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6425 (tm-30) REVERT: B 4549 VAL cc_start: 0.6593 (m) cc_final: 0.6373 (p) REVERT: B 4562 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8345 (mm) REVERT: B 4700 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7678 (mm-40) REVERT: B 4778 TRP cc_start: 0.7335 (OUTLIER) cc_final: 0.5936 (t-100) REVERT: B 4879 MET cc_start: 0.9073 (mmm) cc_final: 0.8815 (tpt) REVERT: B 5031 GLN cc_start: 0.6556 (OUTLIER) cc_final: 0.6349 (tt0) REVERT: C 4180 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7254 (mtm-85) REVERT: C 4232 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6429 (tm-30) REVERT: C 4549 VAL cc_start: 0.6595 (m) cc_final: 0.6367 (p) REVERT: C 4562 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8345 (mm) REVERT: C 4700 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7678 (mm-40) REVERT: C 4778 TRP cc_start: 0.7333 (OUTLIER) cc_final: 0.5923 (t-100) REVERT: C 4879 MET cc_start: 0.9064 (mmm) cc_final: 0.8810 (tpt) REVERT: D 4180 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7249 (mtm-85) REVERT: D 4232 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6417 (tm-30) REVERT: D 4549 VAL cc_start: 0.6605 (m) cc_final: 0.6372 (p) REVERT: D 4562 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8340 (mm) REVERT: D 4700 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7672 (mm-40) REVERT: D 4778 TRP cc_start: 0.7342 (OUTLIER) cc_final: 0.5937 (t-100) REVERT: D 4879 MET cc_start: 0.9067 (mmm) cc_final: 0.8808 (tpt) REVERT: D 5031 GLN cc_start: 0.6544 (OUTLIER) cc_final: 0.6334 (tt0) outliers start: 72 outliers final: 34 residues processed: 338 average time/residue: 1.1158 time to fit residues: 422.3881 Evaluate side-chains 321 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 272 time to evaluate : 1.771 ------------------------------------------------------------------------------- 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 4673 ARG 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 4815 ASP Chi-restraints excluded: chain A residue 4958 CYS Chi-restraints excluded: chain A residue 5014 TYR Chi-restraints excluded: chain A residue 5031 GLN 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 4673 ARG 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 B residue 5031 GLN 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 4673 ARG 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 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 4562 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4631 PHE Chi-restraints excluded: chain D residue 4673 ARG 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 Chi-restraints excluded: chain D residue 5031 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 127 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 137 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.179528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.153226 restraints weight = 17829.607| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.34 r_work: 0.3572 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16276 Z= 0.177 Angle : 0.571 10.305 22192 Z= 0.294 Chirality : 0.038 0.225 2488 Planarity : 0.004 0.043 2736 Dihedral : 9.247 82.312 2364 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.86 % Allowed : 23.42 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.18), residues: 2008 helix: 2.25 (0.13), residues: 1348 sheet: -0.77 (0.49), residues: 104 loop : -0.57 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C4716 HIS 0.008 0.001 HIS B5003 PHE 0.014 0.002 PHE A4916 TYR 0.015 0.002 TYR D4994 ARG 0.011 0.001 ARG D4192 Details of bonding type rmsd hydrogen bonds : bond 0.04225 ( 1106) hydrogen bonds : angle 4.22777 ( 3222) metal coordination : bond 0.01281 ( 16) metal coordination : angle 10.29549 ( 4) SS BOND : bond 0.00238 ( 4) SS BOND : angle 0.66395 ( 8) covalent geometry : bond 0.00400 (16256) covalent geometry : angle 0.55373 (22180) *********************** 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 344 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 273 time to evaluate : 1.661 Fit side-chains REVERT: A 4180 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7211 (mtm-85) REVERT: A 4549 VAL cc_start: 0.6910 (m) cc_final: 0.6680 (p) REVERT: A 4562 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8402 (mm) REVERT: A 4700 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7790 (mm-40) REVERT: A 4778 TRP cc_start: 0.7365 (OUTLIER) cc_final: 0.5930 (t-100) REVERT: A 4879 MET cc_start: 0.9011 (mmm) cc_final: 0.8780 (tpt) REVERT: A 5031 GLN cc_start: 0.6605 (OUTLIER) cc_final: 0.6386 (tt0) REVERT: B 4180 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7245 (mtm-85) REVERT: B 4549 VAL cc_start: 0.6893 (m) cc_final: 0.6680 (p) REVERT: B 4562 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8414 (mm) REVERT: B 4700 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7773 (mm-40) REVERT: B 4778 TRP cc_start: 0.7364 (OUTLIER) cc_final: 0.5927 (t-100) REVERT: B 4879 MET cc_start: 0.9039 (mmm) cc_final: 0.8813 (tpt) REVERT: B 5031 GLN cc_start: 0.6597 (OUTLIER) cc_final: 0.6381 (tt0) REVERT: C 4180 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7216 (mtm-85) REVERT: C 4549 VAL cc_start: 0.6906 (m) cc_final: 0.6686 (p) REVERT: C 4562 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8405 (mm) REVERT: C 4700 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7799 (mm-40) REVERT: C 4778 TRP cc_start: 0.7363 (OUTLIER) cc_final: 0.5928 (t-100) REVERT: C 4879 MET cc_start: 0.9024 (mmm) cc_final: 0.8803 (tpt) REVERT: D 4180 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.7223 (mtm-85) REVERT: D 4549 VAL cc_start: 0.6920 (m) cc_final: 0.6681 (p) REVERT: D 4562 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8411 (mm) REVERT: D 4700 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7794 (mm-40) REVERT: D 4778 TRP cc_start: 0.7370 (OUTLIER) cc_final: 0.5925 (t-100) REVERT: D 4879 MET cc_start: 0.9022 (mmm) cc_final: 0.8797 (tpt) REVERT: D 5031 GLN cc_start: 0.6595 (OUTLIER) cc_final: 0.6375 (tt0) outliers start: 71 outliers final: 44 residues processed: 322 average time/residue: 1.1024 time to fit residues: 397.1520 Evaluate side-chains 333 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 274 time to evaluate : 1.649 ------------------------------------------------------------------------------- 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 4673 ARG 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 4815 ASP Chi-restraints excluded: chain A residue 4958 CYS Chi-restraints excluded: chain A residue 4985 LEU Chi-restraints excluded: chain A residue 5014 TYR Chi-restraints excluded: chain A residue 5031 GLN 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 4662 ASN Chi-restraints excluded: chain B residue 4673 ARG 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 4985 LEU Chi-restraints excluded: chain B residue 5014 TYR Chi-restraints excluded: chain B residue 5031 GLN 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 4673 ARG 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 4815 ASP Chi-restraints excluded: chain C residue 4958 CYS Chi-restraints excluded: chain C residue 4985 LEU 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 4662 ASN Chi-restraints excluded: chain D residue 4673 ARG 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 4985 LEU Chi-restraints excluded: chain D residue 5014 TYR Chi-restraints excluded: chain D residue 5031 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 74 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 193 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 84 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.179424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.152850 restraints weight = 17887.750| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.38 r_work: 0.3565 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16276 Z= 0.170 Angle : 0.575 10.208 22192 Z= 0.296 Chirality : 0.037 0.238 2488 Planarity : 0.004 0.044 2736 Dihedral : 9.137 76.065 2364 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.32 % Allowed : 24.38 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.18), residues: 2008 helix: 2.16 (0.13), residues: 1348 sheet: -0.80 (0.50), residues: 104 loop : -0.53 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A4716 HIS 0.008 0.001 HIS D5003 PHE 0.014 0.002 PHE D4237 TYR 0.016 0.001 TYR D4994 ARG 0.012 0.001 ARG A4192 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 1106) hydrogen bonds : angle 4.26448 ( 3222) metal coordination : bond 0.01239 ( 16) metal coordination : angle 10.20314 ( 4) SS BOND : bond 0.00243 ( 4) SS BOND : angle 0.61243 ( 8) covalent geometry : bond 0.00387 (16256) covalent geometry : angle 0.55814 (22180) *********************** 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 339 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 276 time to evaluate : 1.903 Fit side-chains REVERT: A 4180 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7211 (mtm-85) REVERT: A 4549 VAL cc_start: 0.6873 (m) cc_final: 0.6642 (p) REVERT: A 4562 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8360 (mm) REVERT: A 4700 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7789 (mm-40) REVERT: A 4784 PHE cc_start: 0.8474 (m-80) cc_final: 0.8229 (m-80) REVERT: A 4879 MET cc_start: 0.9016 (mmm) cc_final: 0.8707 (tpt) REVERT: A 5017 ARG cc_start: 0.8157 (mmm160) cc_final: 0.7897 (mmm160) REVERT: A 5031 GLN cc_start: 0.6779 (OUTLIER) cc_final: 0.6540 (tt0) REVERT: B 4180 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7235 (mtm-85) REVERT: B 4549 VAL cc_start: 0.6858 (m) cc_final: 0.6640 (p) REVERT: B 4562 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8416 (mm) REVERT: B 4700 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7791 (mm-40) REVERT: B 4784 PHE cc_start: 0.8469 (m-80) cc_final: 0.8221 (m-80) REVERT: B 4879 MET cc_start: 0.9036 (mmm) cc_final: 0.8733 (tpt) REVERT: B 5017 ARG cc_start: 0.8151 (mmm160) cc_final: 0.7898 (mmm160) REVERT: B 5031 GLN cc_start: 0.6771 (OUTLIER) cc_final: 0.6533 (tt0) REVERT: C 4180 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7215 (mtm-85) REVERT: C 4549 VAL cc_start: 0.6876 (m) cc_final: 0.6652 (p) REVERT: C 4562 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8372 (mm) REVERT: C 4700 GLN cc_start: 0.8065 (mm-40) cc_final: 0.7805 (mm-40) REVERT: C 4784 PHE cc_start: 0.8468 (m-80) cc_final: 0.8221 (m-80) REVERT: C 4879 MET cc_start: 0.9027 (mmm) cc_final: 0.8727 (tpt) REVERT: C 5017 ARG cc_start: 0.8145 (mmm160) cc_final: 0.7887 (mmm160) REVERT: D 4180 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7202 (mtm-85) REVERT: D 4218 ILE cc_start: 0.8091 (pt) cc_final: 0.7660 (mp) REVERT: D 4549 VAL cc_start: 0.6905 (m) cc_final: 0.6666 (p) REVERT: D 4562 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8409 (mm) REVERT: D 4700 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7796 (mm-40) REVERT: D 4784 PHE cc_start: 0.8466 (m-80) cc_final: 0.8223 (m-80) REVERT: D 4879 MET cc_start: 0.9017 (mmm) cc_final: 0.8730 (tpt) REVERT: D 5017 ARG cc_start: 0.8146 (mmm160) cc_final: 0.7891 (mmm160) REVERT: D 5031 GLN cc_start: 0.6769 (OUTLIER) cc_final: 0.6530 (tt0) outliers start: 63 outliers final: 34 residues processed: 321 average time/residue: 1.1009 time to fit residues: 395.2037 Evaluate side-chains 312 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 267 time to evaluate : 1.827 ------------------------------------------------------------------------------- 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 4985 LEU Chi-restraints excluded: chain A residue 5014 TYR Chi-restraints excluded: chain A residue 5031 GLN 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 4958 CYS Chi-restraints excluded: chain B residue 4985 LEU Chi-restraints excluded: chain B residue 5014 TYR Chi-restraints excluded: chain B residue 5031 GLN 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 4958 CYS Chi-restraints excluded: chain C residue 4985 LEU 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 4958 CYS Chi-restraints excluded: chain D residue 4985 LEU Chi-restraints excluded: chain D residue 5014 TYR Chi-restraints excluded: chain D residue 5031 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 44 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 193 optimal weight: 0.9990 chunk 1 optimal weight: 0.0980 chunk 25 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 163 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.179139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.152759 restraints weight = 17783.258| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.34 r_work: 0.3556 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16276 Z= 0.174 Angle : 0.582 10.465 22192 Z= 0.299 Chirality : 0.038 0.219 2488 Planarity : 0.004 0.044 2736 Dihedral : 8.868 71.400 2356 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.25 % Allowed : 25.14 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.18), residues: 2008 helix: 2.15 (0.13), residues: 1348 sheet: -0.86 (0.50), residues: 104 loop : -0.54 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D4716 HIS 0.008 0.001 HIS C5003 PHE 0.019 0.002 PHE D4237 TYR 0.019 0.002 TYR B4630 ARG 0.013 0.001 ARG A4192 Details of bonding type rmsd hydrogen bonds : bond 0.04240 ( 1106) hydrogen bonds : angle 4.29419 ( 3222) metal coordination : bond 0.01264 ( 16) metal coordination : angle 10.45850 ( 4) SS BOND : bond 0.00219 ( 4) SS BOND : angle 0.60462 ( 8) covalent geometry : bond 0.00398 (16256) covalent geometry : angle 0.56455 (22180) *********************** 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: 62 poor density : 273 time to evaluate : 1.829 Fit side-chains REVERT: A 4180 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7100 (mtm-85) REVERT: A 4549 VAL cc_start: 0.6885 (m) cc_final: 0.6650 (p) REVERT: A 4562 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8353 (mm) REVERT: A 4700 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7787 (mm-40) REVERT: A 4704 LEU cc_start: 0.6133 (OUTLIER) cc_final: 0.5494 (pt) REVERT: A 4784 PHE cc_start: 0.8448 (m-80) cc_final: 0.8215 (m-80) REVERT: A 4879 MET cc_start: 0.9015 (mmm) cc_final: 0.8700 (tpt) REVERT: A 5031 GLN cc_start: 0.6698 (OUTLIER) cc_final: 0.6459 (tt0) REVERT: B 4180 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7064 (mtm-85) REVERT: B 4549 VAL cc_start: 0.6869 (m) cc_final: 0.6655 (p) REVERT: B 4700 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7782 (mm-40) REVERT: B 4704 LEU cc_start: 0.6131 (OUTLIER) cc_final: 0.5492 (pt) REVERT: B 4778 TRP cc_start: 0.7363 (OUTLIER) cc_final: 0.5857 (t-100) REVERT: B 4784 PHE cc_start: 0.8440 (m-80) cc_final: 0.8199 (m-80) REVERT: B 4879 MET cc_start: 0.9040 (mmm) cc_final: 0.8730 (tpt) REVERT: B 5031 GLN cc_start: 0.6665 (OUTLIER) cc_final: 0.6442 (tt0) REVERT: C 4180 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7039 (mtm-85) REVERT: C 4549 VAL cc_start: 0.6888 (m) cc_final: 0.6659 (p) REVERT: C 4700 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7793 (mm-40) REVERT: C 4704 LEU cc_start: 0.6133 (OUTLIER) cc_final: 0.5490 (pt) REVERT: C 4784 PHE cc_start: 0.8449 (m-80) cc_final: 0.8214 (m-80) REVERT: C 4879 MET cc_start: 0.9027 (mmm) cc_final: 0.8720 (tpt) REVERT: D 4180 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7009 (mtm-85) REVERT: D 4549 VAL cc_start: 0.6889 (m) cc_final: 0.6646 (p) REVERT: D 4562 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8397 (mm) REVERT: D 4700 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7781 (mm-40) REVERT: D 4704 LEU cc_start: 0.6127 (OUTLIER) cc_final: 0.5488 (pt) REVERT: D 4784 PHE cc_start: 0.8444 (m-80) cc_final: 0.8216 (m-80) REVERT: D 4879 MET cc_start: 0.9028 (mmm) cc_final: 0.8715 (tpt) REVERT: D 5031 GLN cc_start: 0.6663 (OUTLIER) cc_final: 0.6439 (tt0) outliers start: 62 outliers final: 28 residues processed: 321 average time/residue: 1.1647 time to fit residues: 418.6331 Evaluate side-chains 306 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 264 time to evaluate : 2.183 ------------------------------------------------------------------------------- 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 4666 VAL Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4958 CYS Chi-restraints excluded: chain A residue 4985 LEU Chi-restraints excluded: chain A residue 5014 TYR Chi-restraints excluded: chain A residue 5031 GLN 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 4580 TYR Chi-restraints excluded: chain B residue 4631 PHE Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4704 LEU Chi-restraints excluded: chain B residue 4778 TRP Chi-restraints excluded: chain B residue 4958 CYS Chi-restraints excluded: chain B residue 4985 LEU Chi-restraints excluded: chain B residue 5014 TYR Chi-restraints excluded: chain B residue 5031 GLN Chi-restraints excluded: chain C residue 4178 LEU Chi-restraints excluded: chain C residue 4180 ARG 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 4985 LEU 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 4985 LEU Chi-restraints excluded: chain D residue 5014 TYR Chi-restraints excluded: chain D residue 5031 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 21 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 193 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 151 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 49 optimal weight: 0.3980 chunk 22 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.179876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.153371 restraints weight = 17810.118| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 1.37 r_work: 0.3568 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16276 Z= 0.151 Angle : 0.573 9.659 22192 Z= 0.293 Chirality : 0.037 0.253 2488 Planarity : 0.004 0.053 2736 Dihedral : 8.496 65.040 2348 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.97 % Allowed : 25.48 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.18), residues: 2008 helix: 2.18 (0.13), residues: 1348 sheet: -0.91 (0.50), residues: 104 loop : -0.45 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D4716 HIS 0.006 0.001 HIS A5003 PHE 0.012 0.001 PHE C5021 TYR 0.017 0.001 TYR C4630 ARG 0.015 0.001 ARG A4192 Details of bonding type rmsd hydrogen bonds : bond 0.04134 ( 1106) hydrogen bonds : angle 4.25504 ( 3222) metal coordination : bond 0.01104 ( 16) metal coordination : angle 9.64967 ( 4) SS BOND : bond 0.00143 ( 4) SS BOND : angle 0.53216 ( 8) covalent geometry : bond 0.00340 (16256) covalent geometry : angle 0.55791 (22180) *********************** 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 352 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 294 time to evaluate : 1.635 Fit side-chains REVERT: A 4180 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7062 (mtm-85) REVERT: A 4549 VAL cc_start: 0.6845 (m) cc_final: 0.6616 (p) REVERT: A 4700 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7785 (mm-40) REVERT: A 4704 LEU cc_start: 0.6168 (OUTLIER) cc_final: 0.5698 (pt) REVERT: A 4879 MET cc_start: 0.9035 (mmm) cc_final: 0.8725 (tpt) REVERT: B 4180 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7089 (mtm-85) REVERT: B 4549 VAL cc_start: 0.6842 (m) cc_final: 0.6629 (p) REVERT: B 4700 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7780 (mm-40) REVERT: B 4704 LEU cc_start: 0.6166 (OUTLIER) cc_final: 0.5704 (pt) REVERT: B 4879 MET cc_start: 0.9047 (mmm) cc_final: 0.8739 (tpt) REVERT: C 4180 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7056 (mtm-85) REVERT: C 4549 VAL cc_start: 0.6867 (m) cc_final: 0.6637 (p) REVERT: C 4700 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7796 (mm-40) REVERT: C 4704 LEU cc_start: 0.6170 (OUTLIER) cc_final: 0.5698 (pt) REVERT: C 4879 MET cc_start: 0.9048 (mmm) cc_final: 0.8746 (tpt) REVERT: D 4180 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7032 (mtm-85) REVERT: D 4218 ILE cc_start: 0.8080 (pt) cc_final: 0.7623 (mp) REVERT: D 4549 VAL cc_start: 0.6872 (m) cc_final: 0.6632 (p) REVERT: D 4700 GLN cc_start: 0.8064 (mm-40) cc_final: 0.7795 (mm-40) REVERT: D 4704 LEU cc_start: 0.6174 (OUTLIER) cc_final: 0.5702 (pt) REVERT: D 4879 MET cc_start: 0.9043 (mmm) cc_final: 0.8732 (tpt) outliers start: 58 outliers final: 37 residues processed: 334 average time/residue: 1.1351 time to fit residues: 424.0088 Evaluate side-chains 313 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 268 time to evaluate : 1.687 ------------------------------------------------------------------------------- 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 4580 TYR Chi-restraints excluded: chain A residue 4631 PHE Chi-restraints excluded: chain A residue 4662 ASN Chi-restraints excluded: chain A residue 4666 VAL Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4815 ASP Chi-restraints excluded: chain A residue 4958 CYS Chi-restraints excluded: chain A residue 4985 LEU 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 4662 ASN Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4704 LEU Chi-restraints excluded: chain B residue 4958 CYS Chi-restraints excluded: chain B residue 4985 LEU 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 4815 ASP Chi-restraints excluded: chain C residue 4958 CYS Chi-restraints excluded: chain C residue 4985 LEU 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 4666 VAL Chi-restraints excluded: chain D residue 4704 LEU Chi-restraints excluded: chain D residue 4958 CYS Chi-restraints excluded: chain D residue 4985 LEU 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 180 optimal weight: 0.8980 chunk 179 optimal weight: 0.7980 chunk 175 optimal weight: 0.2980 chunk 183 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.179088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.151601 restraints weight = 17947.173| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.41 r_work: 0.3551 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2909 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= 0.176 Angle : 0.601 10.451 22192 Z= 0.308 Chirality : 0.038 0.247 2488 Planarity : 0.004 0.044 2736 Dihedral : 8.278 71.106 2348 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.97 % Allowed : 25.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.18), residues: 2008 helix: 2.09 (0.13), residues: 1348 sheet: -0.98 (0.49), residues: 104 loop : -0.49 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C4205 HIS 0.008 0.001 HIS B5003 PHE 0.038 0.002 PHE A4237 TYR 0.015 0.001 TYR D4994 ARG 0.014 0.001 ARG B4192 Details of bonding type rmsd hydrogen bonds : bond 0.04275 ( 1106) hydrogen bonds : angle 4.32580 ( 3222) metal coordination : bond 0.01250 ( 16) metal coordination : angle 10.43264 ( 4) SS BOND : bond 0.00209 ( 4) SS BOND : angle 0.63673 ( 8) covalent geometry : bond 0.00402 (16256) covalent geometry : angle 0.58437 (22180) ********************** 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 333 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 275 time to evaluate : 2.421 Fit side-chains REVERT: A 4180 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7156 (mtm-85) REVERT: A 4549 VAL cc_start: 0.6955 (m) cc_final: 0.6724 (p) REVERT: A 4700 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7867 (mm-40) REVERT: A 4704 LEU cc_start: 0.6197 (OUTLIER) cc_final: 0.5736 (pt) REVERT: A 4879 MET cc_start: 0.9000 (mmm) cc_final: 0.8711 (tpt) REVERT: B 4180 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7167 (mtm-85) REVERT: B 4549 VAL cc_start: 0.6996 (m) cc_final: 0.6779 (p) REVERT: B 4700 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7863 (mm-40) REVERT: B 4704 LEU cc_start: 0.6196 (OUTLIER) cc_final: 0.5730 (pt) REVERT: B 4879 MET cc_start: 0.9011 (mmm) cc_final: 0.8722 (tpt) REVERT: C 4180 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7130 (mtm-85) REVERT: C 4549 VAL cc_start: 0.7015 (m) cc_final: 0.6784 (p) REVERT: C 4700 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7874 (mm-40) REVERT: C 4704 LEU cc_start: 0.6201 (OUTLIER) cc_final: 0.5738 (pt) REVERT: C 4879 MET cc_start: 0.9007 (mmm) cc_final: 0.8723 (tpt) REVERT: D 4180 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7121 (mtm-85) REVERT: D 4549 VAL cc_start: 0.7016 (m) cc_final: 0.6779 (p) REVERT: D 4700 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7873 (mm-40) REVERT: D 4704 LEU cc_start: 0.6196 (OUTLIER) cc_final: 0.5734 (pt) REVERT: D 4879 MET cc_start: 0.9010 (mmm) cc_final: 0.8721 (tpt) outliers start: 58 outliers final: 38 residues processed: 316 average time/residue: 1.0731 time to fit residues: 381.2576 Evaluate side-chains 314 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 268 time to evaluate : 1.626 ------------------------------------------------------------------------------- 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 4666 VAL Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4815 ASP Chi-restraints excluded: chain A residue 4958 CYS Chi-restraints excluded: chain A residue 4985 LEU 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 4662 ASN Chi-restraints excluded: chain B residue 4666 VAL Chi-restraints excluded: chain B residue 4704 LEU Chi-restraints excluded: chain B residue 4958 CYS Chi-restraints excluded: chain B residue 4985 LEU 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 4815 ASP Chi-restraints excluded: chain C residue 4958 CYS Chi-restraints excluded: chain C residue 4985 LEU 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 4662 ASN Chi-restraints excluded: chain D residue 4704 LEU Chi-restraints excluded: chain D residue 4958 CYS Chi-restraints excluded: chain D residue 4985 LEU 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 92 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 182 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 154 optimal weight: 0.0020 chunk 111 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D5031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.179519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.152368 restraints weight = 17894.142| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.38 r_work: 0.3563 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16276 Z= 0.161 Angle : 0.594 10.093 22192 Z= 0.306 Chirality : 0.038 0.251 2488 Planarity : 0.004 0.043 2736 Dihedral : 8.147 75.645 2348 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.36 % Allowed : 26.71 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.18), residues: 2008 helix: 2.09 (0.13), residues: 1348 sheet: -1.02 (0.49), residues: 104 loop : -0.38 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B4205 HIS 0.007 0.001 HIS B5003 PHE 0.020 0.002 PHE C4237 TYR 0.016 0.001 TYR B4994 ARG 0.014 0.001 ARG B4192 Details of bonding type rmsd hydrogen bonds : bond 0.04207 ( 1106) hydrogen bonds : angle 4.30499 ( 3222) metal coordination : bond 0.01167 ( 16) metal coordination : angle 10.07113 ( 4) SS BOND : bond 0.00142 ( 4) SS BOND : angle 0.58610 ( 8) covalent geometry : bond 0.00369 (16256) covalent geometry : angle 0.57894 (22180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14057.72 seconds wall clock time: 244 minutes 9.20 seconds (14649.20 seconds total)