Starting phenix.real_space_refine on Fri Jul 3 19:05:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qe8_18345/07_2026/8qe8_18345.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qe8_18345/07_2026/8qe8_18345.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qe8_18345/07_2026/8qe8_18345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qe8_18345/07_2026/8qe8_18345.map" model { file = "/net/cci-nas-00/data/ceres_data/8qe8_18345/07_2026/8qe8_18345.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qe8_18345/07_2026/8qe8_18345.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 2 6.06 5 P 2 5.49 5 S 68 5.16 5 C 10095 2.51 5 N 2806 2.21 5 O 2823 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15796 Number of models: 1 Model: "" Number of chains: 12 Chain: "4" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1814 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "5" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1624 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "6" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1605 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "A" Number of atoms: 2831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2831 Classifications: {'peptide': 373} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 13, 'TRANS': 359} Chain breaks: 2 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 12, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 122 Chain: "3" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1812 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 4, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "2" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1628 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "1" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1605 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 2831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2831 Classifications: {'peptide': 373} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 13, 'TRANS': 359} Chain breaks: 2 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 12, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 122 Chain: "4" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'NMN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'NMN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5349 SG CYS A 300 47.022 71.471 134.250 1.00 48.13 S ATOM 5516 SG CYS A 322 47.681 74.983 135.208 1.00 49.47 S ATOM 13225 SG CYS B 300 59.194 49.076 134.315 1.00 48.06 S ATOM 13392 SG CYS B 322 58.509 45.556 135.225 1.00 49.54 S Time building chain proxies: 2.96, per 1000 atoms: 0.19 Number of scatterers: 15796 At special positions: 0 Unit cell: (107.625, 121.975, 180.81, 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 2 29.99 S 68 16.00 P 2 15.00 O 2823 8.00 N 2806 7.00 C 10095 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 701.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" ND1 HIS A 303 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 320 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 322 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 300 " pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" ND1 HIS B 303 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 320 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 322 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 300 " 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: 3860 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 20 sheets defined 37.5% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain '4' and resid 22 through 38 removed outlier: 4.557A pdb=" N PHE 4 28 " --> pdb=" O HIS 4 24 " (cutoff:3.500A) Processing helix chain '4' and resid 52 through 56 removed outlier: 3.534A pdb=" N TYR 4 55 " --> pdb=" O GLY 4 52 " (cutoff:3.500A) Processing helix chain '4' and resid 62 through 74 removed outlier: 3.834A pdb=" N ARG 4 66 " --> pdb=" O PRO 4 62 " (cutoff:3.500A) Processing helix chain '4' and resid 85 through 89 removed outlier: 3.584A pdb=" N LEU 4 88 " --> pdb=" O TRP 4 85 " (cutoff:3.500A) Processing helix chain '4' and resid 94 through 106 Processing helix chain '4' and resid 156 through 163 removed outlier: 4.045A pdb=" N LEU 4 160 " --> pdb=" O GLY 4 156 " (cutoff:3.500A) Processing helix chain '4' and resid 170 through 181 removed outlier: 3.581A pdb=" N TYR 4 181 " --> pdb=" O ILE 4 177 " (cutoff:3.500A) Processing helix chain '4' and resid 189 through 200 removed outlier: 3.864A pdb=" N ALA 4 193 " --> pdb=" O ALA 4 189 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER 4 200 " --> pdb=" O PHE 4 196 " (cutoff:3.500A) Processing helix chain '4' and resid 201 through 206 Processing helix chain '4' and resid 222 through 233 Processing helix chain '4' and resid 241 through 252 Processing helix chain '4' and resid 255 through 260 Processing helix chain '4' and resid 267 through 273 Processing helix chain '5' and resid 21 through 38 removed outlier: 4.019A pdb=" N LEU 5 25 " --> pdb=" O THR 5 21 " (cutoff:3.500A) Processing helix chain '5' and resid 62 through 75 removed outlier: 3.622A pdb=" N ARG 5 66 " --> pdb=" O PRO 5 62 " (cutoff:3.500A) Processing helix chain '5' and resid 94 through 108 removed outlier: 3.517A pdb=" N VAL 5 98 " --> pdb=" O GLU 5 94 " (cutoff:3.500A) Processing helix chain '5' and resid 157 through 163 removed outlier: 4.037A pdb=" N GLU 5 161 " --> pdb=" O ALA 5 157 " (cutoff:3.500A) Processing helix chain '5' and resid 170 through 181 removed outlier: 3.527A pdb=" N TYR 5 181 " --> pdb=" O ILE 5 177 " (cutoff:3.500A) Processing helix chain '5' and resid 189 through 200 removed outlier: 4.111A pdb=" N ALA 5 193 " --> pdb=" O ALA 5 189 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER 5 200 " --> pdb=" O PHE 5 196 " (cutoff:3.500A) Processing helix chain '5' and resid 200 through 206 Processing helix chain '5' and resid 222 through 232 Processing helix chain '5' and resid 241 through 252 Processing helix chain '6' and resid 21 through 38 removed outlier: 4.200A pdb=" N LEU 6 25 " --> pdb=" O THR 6 21 " (cutoff:3.500A) Processing helix chain '6' and resid 52 through 56 removed outlier: 3.897A pdb=" N TYR 6 55 " --> pdb=" O GLY 6 52 " (cutoff:3.500A) Processing helix chain '6' and resid 62 through 74 removed outlier: 3.673A pdb=" N ARG 6 66 " --> pdb=" O PRO 6 62 " (cutoff:3.500A) Processing helix chain '6' and resid 94 through 106 Processing helix chain '6' and resid 156 through 163 removed outlier: 4.009A pdb=" N LEU 6 160 " --> pdb=" O GLY 6 156 " (cutoff:3.500A) Processing helix chain '6' and resid 170 through 181 Processing helix chain '6' and resid 190 through 200 removed outlier: 3.620A pdb=" N GLN 6 194 " --> pdb=" O GLY 6 190 " (cutoff:3.500A) Processing helix chain '6' and resid 200 through 206 Processing helix chain '6' and resid 222 through 232 removed outlier: 3.621A pdb=" N ARG 6 232 " --> pdb=" O ARG 6 228 " (cutoff:3.500A) Processing helix chain '6' and resid 241 through 252 Processing helix chain 'A' and resid 123 through 135 Processing helix chain 'A' and resid 144 through 150 removed outlier: 3.870A pdb=" N GLN A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 300 removed outlier: 3.537A pdb=" N LEU A 288 " --> pdb=" O ARG A 284 " (cutoff:3.500A) Processing helix chain '3' and resid 22 through 38 removed outlier: 4.391A pdb=" N PHE 3 28 " --> pdb=" O HIS 3 24 " (cutoff:3.500A) Processing helix chain '3' and resid 52 through 56 removed outlier: 3.549A pdb=" N TYR 3 55 " --> pdb=" O GLY 3 52 " (cutoff:3.500A) Processing helix chain '3' and resid 62 through 74 removed outlier: 3.845A pdb=" N ARG 3 66 " --> pdb=" O PRO 3 62 " (cutoff:3.500A) Processing helix chain '3' and resid 85 through 89 removed outlier: 3.545A pdb=" N LEU 3 88 " --> pdb=" O TRP 3 85 " (cutoff:3.500A) Processing helix chain '3' and resid 94 through 106 Processing helix chain '3' and resid 156 through 163 removed outlier: 4.025A pdb=" N LEU 3 160 " --> pdb=" O GLY 3 156 " (cutoff:3.500A) Processing helix chain '3' and resid 170 through 181 removed outlier: 3.586A pdb=" N TYR 3 181 " --> pdb=" O ILE 3 177 " (cutoff:3.500A) Processing helix chain '3' and resid 189 through 200 removed outlier: 3.925A pdb=" N ALA 3 193 " --> pdb=" O ALA 3 189 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER 3 200 " --> pdb=" O PHE 3 196 " (cutoff:3.500A) Processing helix chain '3' and resid 201 through 206 Processing helix chain '3' and resid 222 through 233 Processing helix chain '3' and resid 241 through 252 Processing helix chain '3' and resid 255 through 260 Processing helix chain '3' and resid 267 through 273 Processing helix chain '2' and resid 21 through 38 removed outlier: 4.004A pdb=" N LEU 2 25 " --> pdb=" O THR 2 21 " (cutoff:3.500A) Processing helix chain '2' and resid 62 through 75 removed outlier: 3.619A pdb=" N ARG 2 66 " --> pdb=" O PRO 2 62 " (cutoff:3.500A) Processing helix chain '2' and resid 94 through 108 removed outlier: 3.518A pdb=" N VAL 2 98 " --> pdb=" O GLU 2 94 " (cutoff:3.500A) Processing helix chain '2' and resid 157 through 163 removed outlier: 4.030A pdb=" N GLU 2 161 " --> pdb=" O ALA 2 157 " (cutoff:3.500A) Processing helix chain '2' and resid 170 through 181 removed outlier: 3.526A pdb=" N TYR 2 181 " --> pdb=" O ILE 2 177 " (cutoff:3.500A) Processing helix chain '2' and resid 189 through 200 removed outlier: 4.111A pdb=" N ALA 2 193 " --> pdb=" O ALA 2 189 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER 2 200 " --> pdb=" O PHE 2 196 " (cutoff:3.500A) Processing helix chain '2' and resid 200 through 206 Processing helix chain '2' and resid 222 through 232 Processing helix chain '2' and resid 241 through 252 Processing helix chain '1' and resid 21 through 38 removed outlier: 4.191A pdb=" N LEU 1 25 " --> pdb=" O THR 1 21 " (cutoff:3.500A) Processing helix chain '1' and resid 52 through 56 removed outlier: 3.927A pdb=" N TYR 1 55 " --> pdb=" O GLY 1 52 " (cutoff:3.500A) Processing helix chain '1' and resid 62 through 74 removed outlier: 3.673A pdb=" N ARG 1 66 " --> pdb=" O PRO 1 62 " (cutoff:3.500A) Processing helix chain '1' and resid 94 through 106 Processing helix chain '1' and resid 156 through 163 removed outlier: 4.034A pdb=" N LEU 1 160 " --> pdb=" O GLY 1 156 " (cutoff:3.500A) Processing helix chain '1' and resid 170 through 181 Processing helix chain '1' and resid 190 through 200 removed outlier: 3.622A pdb=" N GLN 1 194 " --> pdb=" O GLY 1 190 " (cutoff:3.500A) Processing helix chain '1' and resid 200 through 206 Processing helix chain '1' and resid 222 through 232 removed outlier: 3.614A pdb=" N ARG 1 232 " --> pdb=" O ARG 1 228 " (cutoff:3.500A) Processing helix chain '1' and resid 241 through 252 Processing helix chain 'B' and resid 123 through 135 Processing helix chain 'B' and resid 144 through 150 removed outlier: 3.868A pdb=" N GLN B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 300 removed outlier: 3.537A pdb=" N LEU B 288 " --> pdb=" O ARG B 284 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '4' and resid 80 through 81 removed outlier: 8.302A pdb=" N GLU 4 81 " --> pdb=" O VAL 4 44 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLY 4 46 " --> pdb=" O GLU 4 81 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N THR 4 7 " --> pdb=" O TYR 4 41 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N VAL 4 43 " --> pdb=" O THR 4 7 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL 4 9 " --> pdb=" O VAL 4 43 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS 4 45 " --> pdb=" O VAL 4 9 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLU 4 8 " --> pdb=" O LYS 4 150 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LYS 4 152 " --> pdb=" O GLU 4 8 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL 4 10 " --> pdb=" O LYS 4 152 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU 4 154 " --> pdb=" O VAL 4 10 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU 4 12 " --> pdb=" O LEU 4 154 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL 4 186 " --> pdb=" O CYS 4 155 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU 4 183 " --> pdb=" O HIS 4 211 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL 4 213 " --> pdb=" O LEU 4 183 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N CYS 4 185 " --> pdb=" O VAL 4 213 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '5' and resid 80 through 82 removed outlier: 8.429A pdb=" N GLU 5 81 " --> pdb=" O VAL 5 44 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLY 5 46 " --> pdb=" O GLU 5 81 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N THR 5 7 " --> pdb=" O TYR 5 41 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N VAL 5 43 " --> pdb=" O THR 5 7 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL 5 9 " --> pdb=" O VAL 5 43 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS 5 45 " --> pdb=" O VAL 5 9 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY 5 15 " --> pdb=" O SER 5 49 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLU 5 8 " --> pdb=" O LYS 5 150 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LYS 5 152 " --> pdb=" O GLU 5 8 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL 5 10 " --> pdb=" O LYS 5 152 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU 5 154 " --> pdb=" O VAL 5 10 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU 5 12 " --> pdb=" O LEU 5 154 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU 5 183 " --> pdb=" O HIS 5 211 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N VAL 5 213 " --> pdb=" O LEU 5 183 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N CYS 5 185 " --> pdb=" O VAL 5 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '6' and resid 80 through 82 removed outlier: 8.312A pdb=" N GLU 6 81 " --> pdb=" O VAL 6 44 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLY 6 46 " --> pdb=" O GLU 6 81 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N THR 6 7 " --> pdb=" O TYR 6 41 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N VAL 6 43 " --> pdb=" O THR 6 7 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL 6 9 " --> pdb=" O VAL 6 43 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS 6 45 " --> pdb=" O VAL 6 9 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU 6 8 " --> pdb=" O LYS 6 150 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N LYS 6 152 " --> pdb=" O GLU 6 8 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL 6 10 " --> pdb=" O LYS 6 152 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU 6 154 " --> pdb=" O VAL 6 10 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU 6 12 " --> pdb=" O LEU 6 154 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N ILE 6 184 " --> pdb=" O VAL 6 151 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU 6 153 " --> pdb=" O ILE 6 184 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL 6 186 " --> pdb=" O LEU 6 153 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS 6 155 " --> pdb=" O VAL 6 186 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 333 removed outlier: 5.581A pdb=" N THR A 331 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLY A 626 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN A 333 " --> pdb=" O ILE A 624 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 342 through 347 removed outlier: 7.141A pdb=" N VAL A 363 " --> pdb=" O THR A 380 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N THR A 380 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILE A 365 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 390 through 393 Processing sheet with id=AA7, first strand: chain 'A' and resid 435 through 438 removed outlier: 3.874A pdb=" N THR A 447 " --> pdb=" O TYR A 455 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N PHE A 454 " --> pdb=" O SER A 466 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N SER A 466 " --> pdb=" O PHE A 454 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLN A 456 " --> pdb=" O LEU A 464 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 475 through 477 removed outlier: 6.836A pdb=" N ILE A 493 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 506 " --> pdb=" O ILE A 493 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 513 through 518 removed outlier: 4.269A pdb=" N SER A 515 " --> pdb=" O ASN A 528 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL A 534 " --> pdb=" O LYS A 547 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LYS A 547 " --> pdb=" O VAL A 534 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU A 536 " --> pdb=" O VAL A 545 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 560 through 563 Processing sheet with id=AB2, first strand: chain '3' and resid 80 through 81 removed outlier: 8.315A pdb=" N GLU 3 81 " --> pdb=" O VAL 3 44 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLY 3 46 " --> pdb=" O GLU 3 81 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N THR 3 7 " --> pdb=" O TYR 3 41 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL 3 43 " --> pdb=" O THR 3 7 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL 3 9 " --> pdb=" O VAL 3 43 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS 3 45 " --> pdb=" O VAL 3 9 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU 3 8 " --> pdb=" O LYS 3 150 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LYS 3 152 " --> pdb=" O GLU 3 8 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL 3 10 " --> pdb=" O LYS 3 152 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU 3 154 " --> pdb=" O VAL 3 10 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU 3 12 " --> pdb=" O LEU 3 154 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL 3 186 " --> pdb=" O CYS 3 155 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU 3 183 " --> pdb=" O HIS 3 211 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N VAL 3 213 " --> pdb=" O LEU 3 183 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N CYS 3 185 " --> pdb=" O VAL 3 213 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '2' and resid 80 through 82 removed outlier: 8.442A pdb=" N GLU 2 81 " --> pdb=" O VAL 2 44 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY 2 46 " --> pdb=" O GLU 2 81 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N THR 2 7 " --> pdb=" O TYR 2 41 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N VAL 2 43 " --> pdb=" O THR 2 7 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL 2 9 " --> pdb=" O VAL 2 43 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS 2 45 " --> pdb=" O VAL 2 9 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY 2 15 " --> pdb=" O SER 2 49 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU 2 8 " --> pdb=" O LYS 2 150 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LYS 2 152 " --> pdb=" O GLU 2 8 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL 2 10 " --> pdb=" O LYS 2 152 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU 2 154 " --> pdb=" O VAL 2 10 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU 2 12 " --> pdb=" O LEU 2 154 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU 2 183 " --> pdb=" O HIS 2 211 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N VAL 2 213 " --> pdb=" O LEU 2 183 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N CYS 2 185 " --> pdb=" O VAL 2 213 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '1' and resid 80 through 82 removed outlier: 8.322A pdb=" N GLU 1 81 " --> pdb=" O VAL 1 44 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLY 1 46 " --> pdb=" O GLU 1 81 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N THR 1 7 " --> pdb=" O TYR 1 41 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N VAL 1 43 " --> pdb=" O THR 1 7 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL 1 9 " --> pdb=" O VAL 1 43 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS 1 45 " --> pdb=" O VAL 1 9 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU 1 8 " --> pdb=" O LYS 1 150 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N LYS 1 152 " --> pdb=" O GLU 1 8 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL 1 10 " --> pdb=" O LYS 1 152 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LEU 1 154 " --> pdb=" O VAL 1 10 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU 1 12 " --> pdb=" O LEU 1 154 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N ILE 1 184 " --> pdb=" O VAL 1 151 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU 1 153 " --> pdb=" O ILE 1 184 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N VAL 1 186 " --> pdb=" O LEU 1 153 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N CYS 1 155 " --> pdb=" O VAL 1 186 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 328 through 333 removed outlier: 5.580A pdb=" N THR B 331 " --> pdb=" O GLY B 626 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLY B 626 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN B 333 " --> pdb=" O ILE B 624 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 342 through 347 removed outlier: 7.143A pdb=" N VAL B 363 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N THR B 380 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILE B 365 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 390 through 393 Processing sheet with id=AB8, first strand: chain 'B' and resid 435 through 438 removed outlier: 3.871A pdb=" N THR B 447 " --> pdb=" O TYR B 455 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N PHE B 454 " --> pdb=" O SER B 466 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N SER B 466 " --> pdb=" O PHE B 454 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN B 456 " --> pdb=" O LEU B 464 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 475 through 477 removed outlier: 6.836A pdb=" N ILE B 493 " --> pdb=" O ILE B 506 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE B 506 " --> pdb=" O ILE B 493 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 513 through 518 removed outlier: 4.268A pdb=" N SER B 515 " --> pdb=" O ASN B 528 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL B 534 " --> pdb=" O LYS B 547 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LYS B 547 " --> pdb=" O VAL B 534 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU B 536 " --> pdb=" O VAL B 545 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 560 through 563 604 hydrogen bonds defined for protein. 1746 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5047 1.34 - 1.45: 2322 1.45 - 1.57: 8685 1.57 - 1.69: 2 1.69 - 1.81: 94 Bond restraints: 16150 Sorted by residual: bond pdb=" C SER A 323 " pdb=" N ARG A 324 " ideal model delta sigma weight residual 1.332 1.223 0.108 1.34e-02 5.57e+03 6.54e+01 bond pdb=" O5R NMN 3 501 " pdb=" P NMN 3 501 " ideal model delta sigma weight residual 1.730 1.616 0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" O5R NMN 4 301 " pdb=" P NMN 4 301 " ideal model delta sigma weight residual 1.730 1.616 0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" C5R NMN 4 301 " pdb=" O5R NMN 4 301 " ideal model delta sigma weight residual 1.389 1.451 -0.062 2.00e-02 2.50e+03 9.47e+00 bond pdb=" C5R NMN 3 501 " pdb=" O5R NMN 3 501 " ideal model delta sigma weight residual 1.389 1.451 -0.062 2.00e-02 2.50e+03 9.47e+00 ... (remaining 16145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 21689 2.15 - 4.29: 282 4.29 - 6.44: 24 6.44 - 8.58: 6 8.58 - 10.73: 2 Bond angle restraints: 22003 Sorted by residual: angle pdb=" CA SER A 323 " pdb=" C SER A 323 " pdb=" N ARG A 324 " ideal model delta sigma weight residual 116.21 126.94 -10.73 1.33e+00 5.65e-01 6.51e+01 angle pdb=" O SER A 323 " pdb=" C SER A 323 " pdb=" N ARG A 324 " ideal model delta sigma weight residual 122.93 114.80 8.13 1.23e+00 6.61e-01 4.37e+01 angle pdb=" N ARG A 325 " pdb=" CA ARG A 325 " pdb=" C ARG A 325 " ideal model delta sigma weight residual 111.36 104.33 7.03 1.09e+00 8.42e-01 4.16e+01 angle pdb=" N ARG B 324 " pdb=" CA ARG B 324 " pdb=" C ARG B 324 " ideal model delta sigma weight residual 113.72 106.14 7.58 1.30e+00 5.92e-01 3.40e+01 angle pdb=" N ARG B 325 " pdb=" CA ARG B 325 " pdb=" C ARG B 325 " ideal model delta sigma weight residual 111.28 107.31 3.97 1.09e+00 8.42e-01 1.33e+01 ... (remaining 21998 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 8466 17.29 - 34.59: 844 34.59 - 51.88: 163 51.88 - 69.17: 38 69.17 - 86.47: 24 Dihedral angle restraints: 9535 sinusoidal: 3575 harmonic: 5960 Sorted by residual: dihedral pdb=" CA THR A 362 " pdb=" C THR A 362 " pdb=" N VAL A 363 " pdb=" CA VAL A 363 " ideal model delta harmonic sigma weight residual 180.00 156.10 23.90 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA THR B 362 " pdb=" C THR B 362 " pdb=" N VAL B 363 " pdb=" CA VAL B 363 " ideal model delta harmonic sigma weight residual 180.00 156.11 23.89 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA GLN A 456 " pdb=" C GLN A 456 " pdb=" N CYS A 457 " pdb=" CA CYS A 457 " ideal model delta harmonic sigma weight residual -180.00 -160.69 -19.31 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 9532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2034 0.054 - 0.108: 407 0.108 - 0.163: 95 0.163 - 0.217: 3 0.217 - 0.271: 3 Chirality restraints: 2542 Sorted by residual: chirality pdb=" CA ARG A 325 " pdb=" N ARG A 325 " pdb=" C ARG A 325 " pdb=" CB ARG A 325 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA ARG A 324 " pdb=" N ARG A 324 " pdb=" C ARG A 324 " pdb=" CB ARG A 324 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA ARG B 324 " pdb=" N ARG B 324 " pdb=" C ARG B 324 " pdb=" CB ARG B 324 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 2539 not shown) Planarity restraints: 2753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 605 " 0.018 2.00e-02 2.50e+03 1.87e-02 8.72e+00 pdb=" CG TRP B 605 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP B 605 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP B 605 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 605 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 605 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 605 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 605 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 605 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 605 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 605 " -0.018 2.00e-02 2.50e+03 1.86e-02 8.64e+00 pdb=" CG TRP A 605 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP A 605 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A 605 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 605 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 605 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 605 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 605 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 605 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 605 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL 6 240 " 0.034 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO 6 241 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO 6 241 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO 6 241 " 0.028 5.00e-02 4.00e+02 ... (remaining 2750 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1694 2.75 - 3.29: 14309 3.29 - 3.82: 24336 3.82 - 4.36: 27234 4.36 - 4.90: 49864 Nonbonded interactions: 117437 Sorted by model distance: nonbonded pdb=" OD1 ASN 3 18 " pdb=" OH TYR 3 254 " model vdw 2.210 3.040 nonbonded pdb=" OD1 ASN 4 18 " pdb=" OH TYR 4 254 " model vdw 2.214 3.040 nonbonded pdb=" OD1 ASN 5 18 " pdb=" OH TYR 5 254 " model vdw 2.225 3.040 nonbonded pdb=" OD1 ASN 2 18 " pdb=" OH TYR 2 254 " model vdw 2.243 3.040 nonbonded pdb=" NE2 HIS B 596 " pdb=" OG SER B 615 " model vdw 2.261 3.120 ... (remaining 117432 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '1' and (resid 6 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )) or resid 84 through 103 or (resid 104 through 148 and ( \ name N or name CA or name C or name O or name CB )) or resid 149 through 157 or \ (resid 158 and (name N or name CA or name C or name O or name CB )) or resid 159 \ through 160 or (resid 161 and (name N or name CA or name C or name O or name CB \ )) or resid 162 through 166 or (resid 167 and (name N or name CA or name C or n \ ame O or name CB )) or resid 168 through 172 or (resid 173 and (name N or name C \ A or name C or name O or name CB )) or resid 174 through 187 or (resid 188 throu \ gh 189 and (name N or name CA or name C or name O or name CB )) or resid 190 thr \ ough 194 or (resid 195 and (name N or name CA or name C or name O or name CB )) \ or resid 196 through 204 or (resid 205 and (name N or name CA or name C or name \ O or name CB )) or resid 206 through 214 or (resid 215 and (name N or name CA or \ name C or name O or name CB )) or resid 216 through 255)) selection = (chain '2' and ((resid 6 and (name N or name CA or name C or name O or name CB ) \ ) or resid 7 or (resid 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 through 32 or (resid 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 92 or (resid 93 through 94 and (name N or name \ CA or name C or name O or name CB )) or resid 95 through 96 or (resid 97 and (n \ ame N or name CA or name C or name O or name CB )) or resid 98 through 99 or (re \ sid 100 and (name N or name CA or name C or name O or name CB )) or resid 101 th \ rough 104 or (resid 105 through 106 and (name N or name CA or name C or name O o \ r name CB )) or resid 148 through 169 or (resid 170 and (name N or name CA or na \ me C or name O or name CB )) or resid 171 or (resid 172 through 173 and (name N \ or name CA or name C or name O or name CB )) or resid 174 through 219 or (resid \ 220 and (name N or name CA or name C or name O or name CB )) or resid 221 throug \ h 245 or (resid 246 and (name N or name CA or name C or name O or name CB )) or \ resid 247 through 248 or (resid 249 and (name N or name CA or name C or name O o \ r name CB )) or resid 250 through 255)) selection = (chain '3' and (resid 6 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 32 or (resid 33 and (name N or name CA \ or name C or name O or name CB )) or resid 34 through 55 or (resid 56 through 5 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 59 through 7 \ 7 or (resid 78 and (name N or name CA or name C or name O or name CB )) or resid \ 79 through 80 or (resid 81 and (name N or name CA or name C or name O or name C \ B )) or resid 82 or (resid 83 and (name N or name CA or name C or name O or name \ CB )) or resid 84 through 89 or (resid 90 through 91 and (name N or name CA or \ name C or name O or name CB )) or resid 92 or (resid 93 through 94 and (name N o \ r name CA or name C or name O or name CB )) or resid 95 through 96 or (resid 97 \ and (name N or name CA or name C or name O or name CB )) or resid 98 through 99 \ or (resid 100 and (name N or name CA or name C or name O or name CB )) or resid \ 101 through 103 or (resid 104 through 106 and (name N or name CA or name C or na \ me O or name CB )) or resid 148 through 149 or (resid 150 and (name N or name CA \ or name C or name O or name CB )) or resid 151 through 160 or (resid 161 and (n \ ame N or name CA or name C or name O or name CB )) or resid 162 through 166 or ( \ resid 167 and (name N or name CA or name C or name O or name CB )) or resid 168 \ through 169 or (resid 170 and (name N or name CA or name C or name O or name CB \ )) or resid 171 through 187 or (resid 188 through 189 and (name N or name CA or \ name C or name O or name CB )) or resid 190 through 194 or (resid 195 and (name \ N or name CA or name C or name O or name CB )) or resid 196 through 204 or (resi \ d 205 and (name N or name CA or name C or name O or name CB )) or resid 206 thro \ ugh 214 or (resid 215 and (name N or name CA or name C or name O or name CB )) o \ r resid 216 through 219 or (resid 220 and (name N or name CA or name C or name O \ or name CB )) or resid 221 through 245 or (resid 246 and (name N or name CA or \ name C or name O or name CB )) or resid 247 through 248 or (resid 249 and (name \ N or name CA or name C or name O or name CB )) or resid 250 through 254 or (resi \ d 255 and (name N or name CA or name C or name O or name CB )))) selection = (chain '4' and (resid 6 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 32 or (resid 33 and (name N or name CA \ or name C or name O or name CB )) or resid 34 through 55 or (resid 56 through 5 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 59 through 7 \ 7 or (resid 78 and (name N or name CA or name C or name O or name CB )) or resid \ 79 through 80 or (resid 81 and (name N or name CA or name C or name O or name C \ B )) or resid 82 or (resid 83 and (name N or name CA or name C or name O or name \ CB )) or resid 84 through 89 or (resid 90 through 91 and (name N or name CA or \ name C or name O or name CB )) or resid 92 or (resid 93 through 94 and (name N o \ r name CA or name C or name O or name CB )) or resid 95 through 96 or (resid 97 \ and (name N or name CA or name C or name O or name CB )) or resid 98 through 99 \ or (resid 100 and (name N or name CA or name C or name O or name CB )) or resid \ 101 through 103 or (resid 104 through 106 and (name N or name CA or name C or na \ me O or name CB )) or resid 148 through 149 or (resid 150 and (name N or name CA \ or name C or name O or name CB )) or resid 151 through 160 or (resid 161 and (n \ ame N or name CA or name C or name O or name CB )) or resid 162 through 166 or ( \ resid 167 and (name N or name CA or name C or name O or name CB )) or resid 168 \ through 187 or (resid 188 through 189 and (name N or name CA or name C or name O \ or name CB )) or resid 190 through 194 or (resid 195 and (name N or name CA or \ name C or name O or name CB )) or resid 196 through 204 or (resid 205 and (name \ N or name CA or name C or name O or name CB )) or resid 206 through 214 or (resi \ d 215 and (name N or name CA or name C or name O or name CB )) or resid 216 thro \ ugh 219 or (resid 220 and (name N or name CA or name C or name O or name CB )) o \ r resid 221 through 245 or (resid 246 and (name N or name CA or name C or name O \ or name CB )) or resid 247 through 248 or (resid 249 and (name N or name CA or \ name C or name O or name CB )) or resid 250 through 254 or (resid 255 and (name \ N or name CA or name C or name O or name CB )))) selection = (chain '5' and ((resid 6 and (name N or name CA or name C or name O or name CB ) \ ) or resid 7 or (resid 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 through 32 or (resid 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 92 or (resid 93 through 94 and (name N or name \ CA or name C or name O or name CB )) or resid 95 through 96 or (resid 97 and (n \ ame N or name CA or name C or name O or name CB )) or resid 98 through 99 or (re \ sid 100 and (name N or name CA or name C or name O or name CB )) or resid 101 th \ rough 104 or (resid 105 through 106 and (name N or name CA or name C or name O o \ r name CB )) or resid 148 through 169 or (resid 170 and (name N or name CA or na \ me C or name O or name CB )) or resid 171 or (resid 172 through 173 and (name N \ or name CA or name C or name O or name CB )) or resid 174 through 219 or (resid \ 220 and (name N or name CA or name C or name O or name CB )) or resid 221 throug \ h 248 or (resid 249 and (name N or name CA or name C or name O or name CB )) or \ resid 250 through 255)) selection = (chain '6' and (resid 6 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB )) or resid 84 through 103 or (resid 104 through 148 and ( \ name N or name CA or name C or name O or name CB )) or resid 149 through 157 or \ (resid 158 and (name N or name CA or name C or name O or name CB )) or resid 159 \ through 160 or (resid 161 and (name N or name CA or name C or name O or name CB \ )) or resid 162 through 166 or (resid 167 and (name N or name CA or name C or n \ ame O or name CB )) or resid 168 through 172 or (resid 173 and (name N or name C \ A or name C or name O or name CB )) or resid 174 through 187 or (resid 188 throu \ gh 189 and (name N or name CA or name C or name O or name CB )) or resid 190 thr \ ough 194 or (resid 195 and (name N or name CA or name C or name O or name CB )) \ or resid 196 through 204 or (resid 205 and (name N or name CA or name C or name \ O or name CB )) or resid 206 through 214 or (resid 215 and (name N or name CA or \ name C or name O or name CB )) or resid 216 through 255)) } ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.380 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 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 0.114 16158 Z= 0.211 Angle : 0.631 18.097 22007 Z= 0.337 Chirality : 0.047 0.271 2542 Planarity : 0.004 0.070 2753 Dihedral : 15.045 86.468 5675 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.06 % Allowed : 0.62 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.19), residues: 2008 helix: 1.86 (0.19), residues: 682 sheet: 0.04 (0.23), residues: 504 loop : -1.78 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 4 272 TYR 0.014 0.001 TYR 1 55 PHE 0.027 0.002 PHE 1 163 TRP 0.049 0.001 TRP B 605 HIS 0.004 0.001 HIS B 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.21 (16150) covalent geometry : angle 0.60041 / 0.33 (22003) hydrogen bonds : bond 0.13116 / 9.18 ( 604) hydrogen bonds : angle 5.19568 / 3.81 ( 1746) metal coordination : bond 0.00775 / 0.52 ( 8) metal coordination : angle 14.47297 / 7.00 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.506 Fit side-chains REVERT: 5 220 ASP cc_start: 0.7782 (p0) cc_final: 0.7444 (p0) REVERT: 6 69 MET cc_start: 0.8836 (mtm) cc_final: 0.8577 (mtp) REVERT: 6 83 ASP cc_start: 0.7933 (t0) cc_final: 0.7457 (t0) REVERT: 6 187 THR cc_start: 0.8990 (p) cc_final: 0.8726 (p) REVERT: 2 220 ASP cc_start: 0.7752 (p0) cc_final: 0.7414 (p0) REVERT: 1 69 MET cc_start: 0.8862 (mtm) cc_final: 0.8595 (mtp) REVERT: 1 83 ASP cc_start: 0.7917 (t0) cc_final: 0.7441 (t0) outliers start: 1 outliers final: 1 residues processed: 123 average time/residue: 0.1091 time to fit residues: 21.2681 Evaluate side-chains 96 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 55 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.0050 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.0670 overall best weight: 0.9334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** 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 = 0.3125 r_free = 0.3125 target = 0.086513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.077677 restraints weight = 35931.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.078873 restraints weight = 24606.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.079711 restraints weight = 18487.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.080305 restraints weight = 14842.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.080738 restraints weight = 12565.678| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.0673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16158 Z= 0.132 Angle : 0.516 8.367 22007 Z= 0.274 Chirality : 0.044 0.168 2542 Planarity : 0.004 0.051 2753 Dihedral : 4.927 56.757 2260 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.74 % Allowed : 7.07 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.19), residues: 2008 helix: 2.10 (0.19), residues: 690 sheet: 0.08 (0.23), residues: 504 loop : -1.78 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 5 237 TYR 0.012 0.001 TYR 4 247 PHE 0.016 0.002 PHE 3 163 TRP 0.019 0.001 TRP A 605 HIS 0.004 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (16150) covalent geometry : angle 0.51307 / 0.27 (22003) hydrogen bonds : bond 0.03870 / 2.55 ( 604) hydrogen bonds : angle 4.27948 / 3.16 ( 1746) metal coordination : bond 0.01034 / 0.66 ( 8) metal coordination : angle 4.08806 / 2.24 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.634 Fit side-chains REVERT: 5 220 ASP cc_start: 0.7950 (p0) cc_final: 0.7633 (p0) REVERT: 5 249 GLU cc_start: 0.7258 (tp30) cc_final: 0.6997 (tp30) REVERT: A 568 ASP cc_start: 0.7782 (t0) cc_final: 0.7450 (t0) REVERT: 2 220 ASP cc_start: 0.7947 (p0) cc_final: 0.7623 (p0) REVERT: 2 249 GLU cc_start: 0.7263 (tp30) cc_final: 0.7015 (tp30) REVERT: B 568 ASP cc_start: 0.7770 (t0) cc_final: 0.7472 (t0) outliers start: 12 outliers final: 6 residues processed: 115 average time/residue: 0.1007 time to fit residues: 18.7998 Evaluate side-chains 99 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 155 CYS Chi-restraints excluded: chain 5 residue 38 THR Chi-restraints excluded: chain 5 residue 95 THR Chi-restraints excluded: chain 6 residue 55 TYR Chi-restraints excluded: chain 3 residue 53 ASP Chi-restraints excluded: chain 2 residue 95 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 15 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 123 optimal weight: 0.8980 chunk 80 optimal weight: 0.0670 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 5 176 GLN ** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS 2 176 GLN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.086710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.077756 restraints weight = 36157.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.079002 restraints weight = 24771.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.079851 restraints weight = 18484.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.080409 restraints weight = 14815.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.080883 restraints weight = 12590.747| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 16158 Z= 0.107 Angle : 0.477 8.088 22007 Z= 0.251 Chirality : 0.043 0.168 2542 Planarity : 0.004 0.051 2753 Dihedral : 4.711 57.393 2260 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.62 % Allowed : 9.86 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.19), residues: 2008 helix: 2.32 (0.19), residues: 692 sheet: 0.03 (0.22), residues: 510 loop : -1.72 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 3 272 TYR 0.011 0.001 TYR 4 247 PHE 0.013 0.001 PHE 6 163 TRP 0.014 0.001 TRP B 605 HIS 0.003 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (16150) covalent geometry : angle 0.47480 / 0.25 (22003) hydrogen bonds : bond 0.03393 / 2.23 ( 604) hydrogen bonds : angle 4.00947 / 2.97 ( 1746) metal coordination : bond 0.00699 / 0.45 ( 8) metal coordination : angle 3.76618 / 2.21 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.674 Fit side-chains REVERT: 4 249 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: 5 220 ASP cc_start: 0.8068 (p0) cc_final: 0.7734 (p0) REVERT: 5 249 GLU cc_start: 0.7328 (tp30) cc_final: 0.7103 (tp30) REVERT: A 568 ASP cc_start: 0.7718 (t0) cc_final: 0.7339 (t0) REVERT: 2 220 ASP cc_start: 0.8058 (p0) cc_final: 0.7727 (p0) REVERT: 2 249 GLU cc_start: 0.7327 (tp30) cc_final: 0.7080 (tp30) REVERT: B 568 ASP cc_start: 0.7760 (t0) cc_final: 0.7433 (t0) outliers start: 10 outliers final: 8 residues processed: 113 average time/residue: 0.0995 time to fit residues: 17.9405 Evaluate side-chains 105 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 155 CYS Chi-restraints excluded: chain 4 residue 249 GLU Chi-restraints excluded: chain 5 residue 38 THR Chi-restraints excluded: chain 5 residue 95 THR Chi-restraints excluded: chain 6 residue 102 HIS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain 2 residue 95 THR Chi-restraints excluded: chain 1 residue 102 HIS Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 182 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 175 optimal weight: 6.9990 chunk 198 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 78 optimal weight: 0.1980 chunk 21 optimal weight: 2.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 5 102 HIS A 450 GLN 3 206 HIS B 450 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.080801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.071431 restraints weight = 37213.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.072672 restraints weight = 25508.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.073512 restraints weight = 19206.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.074057 restraints weight = 15560.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.074489 restraints weight = 13342.711| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 16158 Z= 0.250 Angle : 0.614 9.218 22007 Z= 0.321 Chirality : 0.047 0.155 2542 Planarity : 0.005 0.051 2753 Dihedral : 5.226 56.966 2258 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.24 % Allowed : 12.59 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.19), residues: 2008 helix: 1.97 (0.19), residues: 690 sheet: 0.03 (0.23), residues: 488 loop : -1.97 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 2 66 TYR 0.013 0.002 TYR 3 247 PHE 0.028 0.002 PHE B 454 TRP 0.017 0.002 TRP B 605 HIS 0.006 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.25 (16150) covalent geometry : angle 0.61047 / 0.32 (22003) hydrogen bonds : bond 0.05077 / 3.33 ( 604) hydrogen bonds : angle 4.55205 / 3.38 ( 1746) metal coordination : bond 0.01290 / 0.83 ( 8) metal coordination : angle 4.87727 / 2.77 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.584 Fit side-chains REVERT: 5 220 ASP cc_start: 0.8073 (p0) cc_final: 0.7719 (p0) REVERT: 5 252 ASN cc_start: 0.8134 (t0) cc_final: 0.7853 (t0) REVERT: A 568 ASP cc_start: 0.7985 (t0) cc_final: 0.7484 (t0) REVERT: 2 220 ASP cc_start: 0.8066 (p0) cc_final: 0.7727 (p0) REVERT: 2 252 ASN cc_start: 0.8174 (t0) cc_final: 0.7786 (t0) REVERT: B 568 ASP cc_start: 0.7967 (t0) cc_final: 0.7468 (t0) outliers start: 20 outliers final: 15 residues processed: 119 average time/residue: 0.1022 time to fit residues: 19.6512 Evaluate side-chains 105 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 155 CYS Chi-restraints excluded: chain 5 residue 38 THR Chi-restraints excluded: chain 5 residue 95 THR Chi-restraints excluded: chain 5 residue 226 ILE Chi-restraints excluded: chain 6 residue 102 HIS Chi-restraints excluded: chain 6 residue 244 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain 3 residue 9 VAL Chi-restraints excluded: chain 2 residue 38 THR Chi-restraints excluded: chain 2 residue 95 THR Chi-restraints excluded: chain 1 residue 102 HIS Chi-restraints excluded: chain 1 residue 244 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 527 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 118 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 177 optimal weight: 0.9980 chunk 176 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 142 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 5 102 HIS A 565 HIS B 565 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.085310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.076368 restraints weight = 36272.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.077580 restraints weight = 24754.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.078341 restraints weight = 18582.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.078980 restraints weight = 15074.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.079421 restraints weight = 12748.517| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 16158 Z= 0.119 Angle : 0.490 6.456 22007 Z= 0.261 Chirality : 0.043 0.163 2542 Planarity : 0.004 0.050 2753 Dihedral : 4.800 55.065 2258 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.12 % Allowed : 13.77 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.19), residues: 2008 helix: 2.23 (0.19), residues: 692 sheet: 0.02 (0.22), residues: 500 loop : -1.81 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 3 272 TYR 0.011 0.001 TYR 4 247 PHE 0.014 0.001 PHE B 454 TRP 0.009 0.001 TRP B 605 HIS 0.003 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (16150) covalent geometry : angle 0.48796 / 0.26 (22003) hydrogen bonds : bond 0.03457 / 2.27 ( 604) hydrogen bonds : angle 4.08103 / 3.03 ( 1746) metal coordination : bond 0.00741 / 0.47 ( 8) metal coordination : angle 3.50349 / 2.06 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.685 Fit side-chains REVERT: 4 249 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7329 (mp0) REVERT: 5 220 ASP cc_start: 0.8217 (p0) cc_final: 0.7884 (p0) REVERT: A 568 ASP cc_start: 0.7889 (t0) cc_final: 0.7421 (t0) REVERT: 2 220 ASP cc_start: 0.8079 (p0) cc_final: 0.7738 (p0) REVERT: B 568 ASP cc_start: 0.7877 (t0) cc_final: 0.7412 (t0) outliers start: 18 outliers final: 12 residues processed: 121 average time/residue: 0.1031 time to fit residues: 20.2080 Evaluate side-chains 113 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 44 VAL Chi-restraints excluded: chain 4 residue 155 CYS Chi-restraints excluded: chain 4 residue 249 GLU Chi-restraints excluded: chain 5 residue 30 LEU Chi-restraints excluded: chain 5 residue 38 THR Chi-restraints excluded: chain 5 residue 95 THR Chi-restraints excluded: chain 6 residue 154 LEU Chi-restraints excluded: chain 6 residue 244 VAL Chi-restraints excluded: chain 3 residue 9 VAL Chi-restraints excluded: chain 2 residue 38 THR Chi-restraints excluded: chain 2 residue 95 THR Chi-restraints excluded: chain 1 residue 154 LEU Chi-restraints excluded: chain 1 residue 244 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 142 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 191 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.085087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.076106 restraints weight = 36267.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.077352 restraints weight = 25015.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.078190 restraints weight = 18696.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.078714 restraints weight = 15025.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.079179 restraints weight = 12846.644| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 16158 Z= 0.156 Angle : 0.518 7.140 22007 Z= 0.274 Chirality : 0.044 0.165 2542 Planarity : 0.004 0.050 2753 Dihedral : 4.838 53.294 2258 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.61 % Allowed : 15.01 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.19), residues: 2008 helix: 2.21 (0.20), residues: 692 sheet: 0.05 (0.22), residues: 486 loop : -1.86 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 5 237 TYR 0.012 0.001 TYR 4 247 PHE 0.018 0.002 PHE A 454 TRP 0.010 0.001 TRP 6 169 HIS 0.003 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (16150) covalent geometry : angle 0.51520 / 0.27 (22003) hydrogen bonds : bond 0.03954 / 2.59 ( 604) hydrogen bonds : angle 4.19808 / 3.12 ( 1746) metal coordination : bond 0.01040 / 0.67 ( 8) metal coordination : angle 4.00237 / 2.35 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.617 Fit side-chains REVERT: 5 220 ASP cc_start: 0.8251 (p0) cc_final: 0.7899 (p0) REVERT: A 568 ASP cc_start: 0.7905 (t0) cc_final: 0.7402 (t0) REVERT: 2 220 ASP cc_start: 0.8080 (p0) cc_final: 0.7706 (p0) REVERT: B 568 ASP cc_start: 0.7892 (t0) cc_final: 0.7386 (t0) outliers start: 26 outliers final: 17 residues processed: 129 average time/residue: 0.1043 time to fit residues: 21.8052 Evaluate side-chains 113 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 44 VAL Chi-restraints excluded: chain 4 residue 155 CYS Chi-restraints excluded: chain 5 residue 30 LEU Chi-restraints excluded: chain 5 residue 38 THR Chi-restraints excluded: chain 5 residue 95 THR Chi-restraints excluded: chain 6 residue 102 HIS Chi-restraints excluded: chain 6 residue 154 LEU Chi-restraints excluded: chain 6 residue 244 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain 3 residue 9 VAL Chi-restraints excluded: chain 2 residue 30 LEU Chi-restraints excluded: chain 2 residue 38 THR Chi-restraints excluded: chain 2 residue 95 THR Chi-restraints excluded: chain 1 residue 102 HIS Chi-restraints excluded: chain 1 residue 154 LEU Chi-restraints excluded: chain 1 residue 244 VAL Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 27 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 167 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 198 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 129 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.086315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.077816 restraints weight = 35823.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.078924 restraints weight = 24901.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.079684 restraints weight = 18931.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.080238 restraints weight = 15428.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.080621 restraints weight = 13173.365| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 16158 Z= 0.121 Angle : 0.491 6.461 22007 Z= 0.261 Chirality : 0.043 0.164 2542 Planarity : 0.004 0.049 2753 Dihedral : 4.687 51.815 2258 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.30 % Allowed : 15.94 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.19), residues: 2008 helix: 2.32 (0.20), residues: 692 sheet: -0.02 (0.22), residues: 498 loop : -1.73 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 5 237 TYR 0.011 0.001 TYR 4 247 PHE 0.013 0.001 PHE A 454 TRP 0.009 0.001 TRP B 582 HIS 0.003 0.001 HIS B 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (16150) covalent geometry : angle 0.48836 / 0.26 (22003) hydrogen bonds : bond 0.03429 / 2.24 ( 604) hydrogen bonds : angle 4.02655 / 2.99 ( 1746) metal coordination : bond 0.00886 / 0.58 ( 8) metal coordination : angle 3.52881 / 2.08 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.531 Fit side-chains REVERT: 4 249 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7819 (mp0) REVERT: 5 220 ASP cc_start: 0.8255 (p0) cc_final: 0.7896 (p0) REVERT: A 568 ASP cc_start: 0.7876 (t0) cc_final: 0.7391 (t0) REVERT: 2 220 ASP cc_start: 0.8064 (p0) cc_final: 0.7709 (p0) REVERT: 2 252 ASN cc_start: 0.8143 (t0) cc_final: 0.7904 (t0) REVERT: B 568 ASP cc_start: 0.7867 (t0) cc_final: 0.7382 (t0) outliers start: 21 outliers final: 14 residues processed: 117 average time/residue: 0.1071 time to fit residues: 20.1882 Evaluate side-chains 113 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 44 VAL Chi-restraints excluded: chain 4 residue 155 CYS Chi-restraints excluded: chain 4 residue 249 GLU Chi-restraints excluded: chain 5 residue 30 LEU Chi-restraints excluded: chain 5 residue 38 THR Chi-restraints excluded: chain 5 residue 95 THR Chi-restraints excluded: chain 6 residue 154 LEU Chi-restraints excluded: chain 6 residue 244 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain 3 residue 9 VAL Chi-restraints excluded: chain 2 residue 30 LEU Chi-restraints excluded: chain 2 residue 38 THR Chi-restraints excluded: chain 2 residue 95 THR Chi-restraints excluded: chain 1 residue 154 LEU Chi-restraints excluded: chain 1 residue 244 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 78 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 5 102 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.083070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.074217 restraints weight = 36567.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.075393 restraints weight = 25078.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.076184 restraints weight = 18871.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.076764 restraints weight = 15294.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.077182 restraints weight = 13028.965| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 16158 Z= 0.244 Angle : 0.608 9.551 22007 Z= 0.320 Chirality : 0.047 0.166 2542 Planarity : 0.005 0.050 2753 Dihedral : 5.146 50.832 2258 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.61 % Allowed : 16.81 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.19), residues: 2008 helix: 1.92 (0.19), residues: 690 sheet: -0.04 (0.22), residues: 488 loop : -2.00 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 2 66 TYR 0.013 0.002 TYR 4 247 PHE 0.024 0.002 PHE A 454 TRP 0.012 0.002 TRP 6 169 HIS 0.005 0.001 HIS A 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.24 (16150) covalent geometry : angle 0.60491 / 0.32 (22003) hydrogen bonds : bond 0.04927 / 3.22 ( 604) hydrogen bonds : angle 4.51072 / 3.35 ( 1746) metal coordination : bond 0.01483 / 0.97 ( 8) metal coordination : angle 4.78208 / 2.76 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.510 Fit side-chains REVERT: 4 249 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7774 (mp0) REVERT: 5 220 ASP cc_start: 0.8263 (p0) cc_final: 0.7917 (p0) REVERT: A 568 ASP cc_start: 0.8006 (t0) cc_final: 0.7450 (t0) REVERT: 2 220 ASP cc_start: 0.8075 (p0) cc_final: 0.7729 (p0) REVERT: 2 252 ASN cc_start: 0.8175 (t0) cc_final: 0.7799 (t0) REVERT: B 568 ASP cc_start: 0.7991 (t0) cc_final: 0.7432 (t0) outliers start: 26 outliers final: 23 residues processed: 123 average time/residue: 0.1063 time to fit residues: 20.9153 Evaluate side-chains 119 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 44 VAL Chi-restraints excluded: chain 4 residue 155 CYS Chi-restraints excluded: chain 4 residue 249 GLU Chi-restraints excluded: chain 4 residue 253 LEU Chi-restraints excluded: chain 5 residue 23 MET Chi-restraints excluded: chain 5 residue 30 LEU Chi-restraints excluded: chain 5 residue 38 THR Chi-restraints excluded: chain 5 residue 95 THR Chi-restraints excluded: chain 6 residue 9 VAL Chi-restraints excluded: chain 6 residue 102 HIS Chi-restraints excluded: chain 6 residue 154 LEU Chi-restraints excluded: chain 6 residue 244 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain 3 residue 9 VAL Chi-restraints excluded: chain 2 residue 30 LEU Chi-restraints excluded: chain 2 residue 38 THR Chi-restraints excluded: chain 2 residue 95 THR Chi-restraints excluded: chain 1 residue 9 VAL Chi-restraints excluded: chain 1 residue 102 HIS Chi-restraints excluded: chain 1 residue 154 LEU Chi-restraints excluded: chain 1 residue 244 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 527 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 137 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 187 optimal weight: 0.0970 chunk 16 optimal weight: 0.6980 chunk 129 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 5 102 HIS 5 252 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.086110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.077359 restraints weight = 35825.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.078555 restraints weight = 24353.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.079377 restraints weight = 18215.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.079953 restraints weight = 14634.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.080396 restraints weight = 12398.198| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16158 Z= 0.109 Angle : 0.488 6.781 22007 Z= 0.261 Chirality : 0.043 0.165 2542 Planarity : 0.004 0.048 2753 Dihedral : 4.689 50.484 2258 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.18 % Allowed : 17.37 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.19), residues: 2008 helix: 2.24 (0.20), residues: 692 sheet: -0.02 (0.23), residues: 486 loop : -1.79 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 4 272 TYR 0.011 0.001 TYR 4 247 PHE 0.014 0.001 PHE 1 163 TRP 0.009 0.001 TRP B 582 HIS 0.002 0.001 HIS 4 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (16150) covalent geometry : angle 0.48611 / 0.26 (22003) hydrogen bonds : bond 0.03256 / 2.13 ( 604) hydrogen bonds : angle 4.03353 / 3.00 ( 1746) metal coordination : bond 0.00835 / 0.56 ( 8) metal coordination : angle 3.36371 / 1.98 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.697 Fit side-chains REVERT: 4 249 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: 5 220 ASP cc_start: 0.8267 (p0) cc_final: 0.7932 (p0) REVERT: A 568 ASP cc_start: 0.7891 (t0) cc_final: 0.7396 (t0) REVERT: 2 220 ASP cc_start: 0.8084 (p0) cc_final: 0.7735 (p0) REVERT: 2 252 ASN cc_start: 0.8107 (t0) cc_final: 0.7898 (t0) REVERT: B 568 ASP cc_start: 0.7847 (t0) cc_final: 0.7361 (t0) outliers start: 19 outliers final: 15 residues processed: 122 average time/residue: 0.0915 time to fit residues: 17.9127 Evaluate side-chains 115 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 44 VAL Chi-restraints excluded: chain 4 residue 155 CYS Chi-restraints excluded: chain 4 residue 249 GLU Chi-restraints excluded: chain 5 residue 38 THR Chi-restraints excluded: chain 5 residue 95 THR Chi-restraints excluded: chain 6 residue 154 LEU Chi-restraints excluded: chain 6 residue 244 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain 3 residue 9 VAL Chi-restraints excluded: chain 2 residue 30 LEU Chi-restraints excluded: chain 2 residue 38 THR Chi-restraints excluded: chain 2 residue 95 THR Chi-restraints excluded: chain 1 residue 9 VAL Chi-restraints excluded: chain 1 residue 154 LEU Chi-restraints excluded: chain 1 residue 244 VAL Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 103 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 97 optimal weight: 0.0770 chunk 49 optimal weight: 2.9990 chunk 188 optimal weight: 0.0010 chunk 42 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 116 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.4544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 5 252 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.087931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.079192 restraints weight = 35599.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.080402 restraints weight = 24069.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.081185 restraints weight = 17968.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.081816 restraints weight = 14544.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.082189 restraints weight = 12219.209| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16158 Z= 0.088 Angle : 0.455 6.803 22007 Z= 0.244 Chirality : 0.042 0.162 2542 Planarity : 0.004 0.048 2753 Dihedral : 4.358 47.762 2258 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.99 % Allowed : 17.68 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.19), residues: 2008 helix: 2.43 (0.20), residues: 692 sheet: 0.02 (0.23), residues: 504 loop : -1.67 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 4 272 TYR 0.009 0.001 TYR 4 247 PHE 0.010 0.001 PHE 1 163 TRP 0.007 0.001 TRP 5 85 HIS 0.003 0.001 HIS B 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 (16150) covalent geometry : angle 0.45310 / 0.24 (22003) hydrogen bonds : bond 0.02757 / 1.79 ( 604) hydrogen bonds : angle 3.81473 / 2.83 ( 1746) metal coordination : bond 0.00794 / 0.54 ( 8) metal coordination : angle 3.30524 / 1.91 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.636 Fit side-chains REVERT: 5 220 ASP cc_start: 0.8251 (p0) cc_final: 0.7915 (p0) REVERT: 6 86 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7140 (mt-10) REVERT: A 568 ASP cc_start: 0.7869 (t0) cc_final: 0.7414 (t0) REVERT: 2 220 ASP cc_start: 0.8104 (p0) cc_final: 0.7768 (p0) REVERT: B 568 ASP cc_start: 0.7864 (t0) cc_final: 0.7407 (t0) outliers start: 16 outliers final: 13 residues processed: 130 average time/residue: 0.0950 time to fit residues: 20.1225 Evaluate side-chains 122 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 155 CYS Chi-restraints excluded: chain 5 residue 38 THR Chi-restraints excluded: chain 5 residue 95 THR Chi-restraints excluded: chain 6 residue 154 LEU Chi-restraints excluded: chain 6 residue 244 VAL Chi-restraints excluded: chain 3 residue 9 VAL Chi-restraints excluded: chain 2 residue 30 LEU Chi-restraints excluded: chain 2 residue 38 THR Chi-restraints excluded: chain 2 residue 95 THR Chi-restraints excluded: chain 1 residue 9 VAL Chi-restraints excluded: chain 1 residue 154 LEU Chi-restraints excluded: chain 1 residue 244 VAL Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 10 optimal weight: 0.2980 chunk 115 optimal weight: 0.7980 chunk 175 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 5 252 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.086984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.078218 restraints weight = 35607.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.079431 restraints weight = 24009.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.080262 restraints weight = 17943.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.080857 restraints weight = 14399.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.081236 restraints weight = 12138.373| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16158 Z= 0.113 Angle : 0.483 6.288 22007 Z= 0.258 Chirality : 0.043 0.161 2542 Planarity : 0.004 0.049 2753 Dihedral : 4.475 48.270 2258 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.99 % Allowed : 18.05 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.19), residues: 2008 helix: 2.40 (0.20), residues: 692 sheet: 0.17 (0.23), residues: 486 loop : -1.68 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 4 272 TYR 0.011 0.001 TYR 4 247 PHE 0.012 0.001 PHE A 454 TRP 0.009 0.001 TRP B 582 HIS 0.003 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 (16150) covalent geometry : angle 0.48107 / 0.26 (22003) hydrogen bonds : bond 0.03228 / 2.10 ( 604) hydrogen bonds : angle 3.90592 / 2.91 ( 1746) metal coordination : bond 0.00966 / 0.65 ( 8) metal coordination : angle 3.52880 / 2.07 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1937.90 seconds wall clock time: 34 minutes 36.12 seconds (2076.12 seconds total)