Starting phenix.real_space_refine on Fri Jun 13 01:51:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ckw_16704/06_2025/8ckw_16704.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ckw_16704/06_2025/8ckw_16704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ckw_16704/06_2025/8ckw_16704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ckw_16704/06_2025/8ckw_16704.map" model { file = "/net/cci-nas-00/data/ceres_data/8ckw_16704/06_2025/8ckw_16704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ckw_16704/06_2025/8ckw_16704.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1045 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 8745 2.51 5 N 2390 2.21 5 O 2650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13890 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1612 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "C" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "D" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1612 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "F" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "G" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1612 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "I" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "J" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1612 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "K" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "L" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "M" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1612 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "N" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "O" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Time building chain proxies: 9.63, per 1000 atoms: 0.69 Number of scatterers: 13890 At special positions: 0 Unit cell: (148.8, 153.45, 95.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 2650 8.00 N 2390 7.00 C 8745 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: 3.48 Conformation dependent library (CDL) restraints added in 1.6 seconds 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3360 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 5 sheets defined 74.8% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 16 through 30 Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 57 Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 125 through 145 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 160 through 174 Processing helix chain 'A' and resid 178 through 193 removed outlier: 4.254A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 removed outlier: 3.622A pdb=" N ILE A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 160 through 173 Processing helix chain 'B' and resid 178 through 193 removed outlier: 3.555A pdb=" N TRP B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 205 removed outlier: 3.839A pdb=" N ALA B 204 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 160 through 176 removed outlier: 3.609A pdb=" N GLN C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 193 removed outlier: 4.613A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 205 removed outlier: 3.609A pdb=" N LEU C 205 " --> pdb=" O ILE C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 219 Processing helix chain 'D' and resid 16 through 30 Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 48 through 57 Processing helix chain 'D' and resid 62 through 84 Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 110 through 120 Processing helix chain 'D' and resid 125 through 145 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 160 through 174 Processing helix chain 'D' and resid 178 through 193 removed outlier: 4.255A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 removed outlier: 3.622A pdb=" N ILE D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 219 Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 160 through 173 Processing helix chain 'E' and resid 178 through 193 removed outlier: 3.555A pdb=" N TRP E 184 " --> pdb=" O GLU E 180 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 205 removed outlier: 3.839A pdb=" N ALA E 204 " --> pdb=" O THR E 200 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU E 205 " --> pdb=" O ILE E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 218 Processing helix chain 'F' and resid 149 through 153 Processing helix chain 'F' and resid 160 through 176 removed outlier: 3.609A pdb=" N GLN F 176 " --> pdb=" O LEU F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 193 removed outlier: 4.613A pdb=" N LEU F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 205 removed outlier: 3.610A pdb=" N LEU F 205 " --> pdb=" O ILE F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 219 Processing helix chain 'G' and resid 16 through 30 Processing helix chain 'G' and resid 35 through 44 Processing helix chain 'G' and resid 48 through 57 Processing helix chain 'G' and resid 62 through 84 Processing helix chain 'G' and resid 100 through 105 Processing helix chain 'G' and resid 110 through 120 Processing helix chain 'G' and resid 125 through 145 Processing helix chain 'G' and resid 149 through 153 Processing helix chain 'G' and resid 160 through 174 Processing helix chain 'G' and resid 178 through 193 removed outlier: 4.254A pdb=" N LEU G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL G 191 " --> pdb=" O GLU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 205 removed outlier: 3.622A pdb=" N ILE G 201 " --> pdb=" O ASP G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 219 Processing helix chain 'H' and resid 149 through 153 Processing helix chain 'H' and resid 160 through 173 Processing helix chain 'H' and resid 178 through 193 removed outlier: 3.555A pdb=" N TRP H 184 " --> pdb=" O GLU H 180 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU H 190 " --> pdb=" O THR H 186 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL H 191 " --> pdb=" O GLU H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 205 removed outlier: 3.839A pdb=" N ALA H 204 " --> pdb=" O THR H 200 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU H 205 " --> pdb=" O ILE H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 218 Processing helix chain 'I' and resid 149 through 153 Processing helix chain 'I' and resid 160 through 176 removed outlier: 3.610A pdb=" N GLN I 176 " --> pdb=" O LEU I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 193 removed outlier: 4.613A pdb=" N LEU I 190 " --> pdb=" O THR I 186 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL I 191 " --> pdb=" O GLU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 205 removed outlier: 3.609A pdb=" N LEU I 205 " --> pdb=" O ILE I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 219 Processing helix chain 'J' and resid 16 through 30 Processing helix chain 'J' and resid 35 through 44 Processing helix chain 'J' and resid 48 through 57 Processing helix chain 'J' and resid 62 through 84 Processing helix chain 'J' and resid 100 through 105 Processing helix chain 'J' and resid 110 through 120 Processing helix chain 'J' and resid 125 through 145 Processing helix chain 'J' and resid 149 through 153 Processing helix chain 'J' and resid 160 through 174 Processing helix chain 'J' and resid 178 through 193 removed outlier: 4.254A pdb=" N LEU J 190 " --> pdb=" O THR J 186 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL J 191 " --> pdb=" O GLU J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 205 removed outlier: 3.622A pdb=" N ILE J 201 " --> pdb=" O ASP J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 219 Processing helix chain 'K' and resid 149 through 153 Processing helix chain 'K' and resid 160 through 173 Processing helix chain 'K' and resid 178 through 193 removed outlier: 3.555A pdb=" N TRP K 184 " --> pdb=" O GLU K 180 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU K 190 " --> pdb=" O THR K 186 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL K 191 " --> pdb=" O GLU K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 205 removed outlier: 3.839A pdb=" N ALA K 204 " --> pdb=" O THR K 200 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU K 205 " --> pdb=" O ILE K 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 218 Processing helix chain 'L' and resid 149 through 153 Processing helix chain 'L' and resid 160 through 176 removed outlier: 3.609A pdb=" N GLN L 176 " --> pdb=" O LEU L 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 178 through 193 removed outlier: 4.613A pdb=" N LEU L 190 " --> pdb=" O THR L 186 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL L 191 " --> pdb=" O GLU L 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 205 removed outlier: 3.609A pdb=" N LEU L 205 " --> pdb=" O ILE L 201 " (cutoff:3.500A) Processing helix chain 'L' and resid 210 through 219 Processing helix chain 'M' and resid 16 through 30 Processing helix chain 'M' and resid 35 through 44 Processing helix chain 'M' and resid 48 through 57 Processing helix chain 'M' and resid 62 through 84 Processing helix chain 'M' and resid 100 through 105 Processing helix chain 'M' and resid 110 through 120 Processing helix chain 'M' and resid 125 through 145 Processing helix chain 'M' and resid 149 through 153 Processing helix chain 'M' and resid 160 through 174 Processing helix chain 'M' and resid 178 through 193 removed outlier: 4.254A pdb=" N LEU M 190 " --> pdb=" O THR M 186 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N VAL M 191 " --> pdb=" O GLU M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 205 removed outlier: 3.622A pdb=" N ILE M 201 " --> pdb=" O ASP M 197 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 219 Processing helix chain 'N' and resid 149 through 153 Processing helix chain 'N' and resid 160 through 173 Processing helix chain 'N' and resid 178 through 193 removed outlier: 3.555A pdb=" N TRP N 184 " --> pdb=" O GLU N 180 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU N 190 " --> pdb=" O THR N 186 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL N 191 " --> pdb=" O GLU N 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 195 through 205 removed outlier: 3.839A pdb=" N ALA N 204 " --> pdb=" O THR N 200 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU N 205 " --> pdb=" O ILE N 201 " (cutoff:3.500A) Processing helix chain 'N' and resid 210 through 218 Processing helix chain 'O' and resid 149 through 153 Processing helix chain 'O' and resid 160 through 176 removed outlier: 3.609A pdb=" N GLN O 176 " --> pdb=" O LEU O 172 " (cutoff:3.500A) Processing helix chain 'O' and resid 178 through 193 removed outlier: 4.613A pdb=" N LEU O 190 " --> pdb=" O THR O 186 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL O 191 " --> pdb=" O GLU O 187 " (cutoff:3.500A) Processing helix chain 'O' and resid 195 through 205 removed outlier: 3.609A pdb=" N LEU O 205 " --> pdb=" O ILE O 201 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 219 Processing sheet with id=1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=2, first strand: chain 'D' and resid 2 through 4 Processing sheet with id=3, first strand: chain 'G' and resid 2 through 4 Processing sheet with id=4, first strand: chain 'J' and resid 2 through 4 Processing sheet with id=5, first strand: chain 'M' and resid 2 through 4 860 hydrogen bonds defined for protein. 2490 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.76 Time building geometry restraints manager: 4.12 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: 4582 1.34 - 1.46: 1359 1.46 - 1.57: 8034 1.57 - 1.69: 0 1.69 - 1.81: 180 Bond restraints: 14155 Sorted by residual: bond pdb=" N THR F 148 " pdb=" CA THR F 148 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.90e-02 2.77e+03 4.08e+00 bond pdb=" N THR I 148 " pdb=" CA THR I 148 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.90e-02 2.77e+03 3.94e+00 bond pdb=" N THR C 148 " pdb=" CA THR C 148 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.90e-02 2.77e+03 3.94e+00 bond pdb=" N THR L 148 " pdb=" CA THR L 148 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.90e-02 2.77e+03 3.89e+00 bond pdb=" N THR O 148 " pdb=" CA THR O 148 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.90e-02 2.77e+03 3.85e+00 ... (remaining 14150 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 18924 2.74 - 5.48: 276 5.48 - 8.22: 0 8.22 - 10.96: 0 10.96 - 13.69: 5 Bond angle restraints: 19205 Sorted by residual: angle pdb=" CB LEU J 83 " pdb=" CG LEU J 83 " pdb=" CD1 LEU J 83 " ideal model delta sigma weight residual 110.70 124.39 -13.69 3.00e+00 1.11e-01 2.08e+01 angle pdb=" CB LEU A 83 " pdb=" CG LEU A 83 " pdb=" CD1 LEU A 83 " ideal model delta sigma weight residual 110.70 124.38 -13.68 3.00e+00 1.11e-01 2.08e+01 angle pdb=" CB LEU M 83 " pdb=" CG LEU M 83 " pdb=" CD1 LEU M 83 " ideal model delta sigma weight residual 110.70 124.37 -13.67 3.00e+00 1.11e-01 2.08e+01 angle pdb=" CB LEU D 83 " pdb=" CG LEU D 83 " pdb=" CD1 LEU D 83 " ideal model delta sigma weight residual 110.70 124.36 -13.66 3.00e+00 1.11e-01 2.07e+01 angle pdb=" CB LEU G 83 " pdb=" CG LEU G 83 " pdb=" CD1 LEU G 83 " ideal model delta sigma weight residual 110.70 124.36 -13.66 3.00e+00 1.11e-01 2.07e+01 ... (remaining 19200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.63: 7908 15.63 - 31.27: 617 31.27 - 46.90: 120 46.90 - 62.54: 35 62.54 - 78.17: 20 Dihedral angle restraints: 8700 sinusoidal: 3535 harmonic: 5165 Sorted by residual: dihedral pdb=" CA THR G 148 " pdb=" C THR G 148 " pdb=" N SER G 149 " pdb=" CA SER G 149 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA THR D 148 " pdb=" C THR D 148 " pdb=" N SER D 149 " pdb=" CA SER D 149 " ideal model delta harmonic sigma weight residual 180.00 159.89 20.11 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA THR M 148 " pdb=" C THR M 148 " pdb=" N SER M 149 " pdb=" CA SER M 149 " ideal model delta harmonic sigma weight residual 180.00 159.90 20.10 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 8697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.246: 2180 0.246 - 0.492: 0 0.492 - 0.739: 0 0.739 - 0.985: 0 0.985 - 1.231: 5 Chirality restraints: 2185 Sorted by residual: chirality pdb=" CG LEU M 83 " pdb=" CB LEU M 83 " pdb=" CD1 LEU M 83 " pdb=" CD2 LEU M 83 " both_signs ideal model delta sigma weight residual False -2.59 -1.36 -1.23 2.00e-01 2.50e+01 3.79e+01 chirality pdb=" CG LEU D 83 " pdb=" CB LEU D 83 " pdb=" CD1 LEU D 83 " pdb=" CD2 LEU D 83 " both_signs ideal model delta sigma weight residual False -2.59 -1.36 -1.23 2.00e-01 2.50e+01 3.79e+01 chirality pdb=" CG LEU A 83 " pdb=" CB LEU A 83 " pdb=" CD1 LEU A 83 " pdb=" CD2 LEU A 83 " both_signs ideal model delta sigma weight residual False -2.59 -1.36 -1.23 2.00e-01 2.50e+01 3.79e+01 ... (remaining 2182 not shown) Planarity restraints: 2490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG J 18 " 0.013 2.00e-02 2.50e+03 2.52e-02 6.37e+00 pdb=" C ARG J 18 " -0.044 2.00e-02 2.50e+03 pdb=" O ARG J 18 " 0.016 2.00e-02 2.50e+03 pdb=" N THR J 19 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG M 18 " 0.013 2.00e-02 2.50e+03 2.52e-02 6.36e+00 pdb=" C ARG M 18 " -0.044 2.00e-02 2.50e+03 pdb=" O ARG M 18 " 0.016 2.00e-02 2.50e+03 pdb=" N THR M 19 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 18 " -0.013 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" C ARG A 18 " 0.043 2.00e-02 2.50e+03 pdb=" O ARG A 18 " -0.016 2.00e-02 2.50e+03 pdb=" N THR A 19 " -0.015 2.00e-02 2.50e+03 ... (remaining 2487 not shown) Histogram of nonbonded interaction distances: 0.52 - 1.40: 5 1.40 - 2.27: 15 2.27 - 3.15: 12004 3.15 - 4.02: 36391 4.02 - 4.90: 66385 Warning: very small nonbonded interaction distances. Nonbonded interactions: 114800 Sorted by model distance: nonbonded pdb=" CD1 LEU J 20 " pdb=" OE2 GLU M 45 " model vdw 0.523 3.460 nonbonded pdb=" CD1 LEU G 20 " pdb=" OE2 GLU J 45 " model vdw 0.524 3.460 nonbonded pdb=" OE2 GLU A 45 " pdb=" CD1 LEU M 20 " model vdw 0.524 3.460 nonbonded pdb=" CD1 LEU D 20 " pdb=" OE2 GLU G 45 " model vdw 0.524 3.460 nonbonded pdb=" CD1 LEU A 20 " pdb=" OE2 GLU D 45 " model vdw 0.524 3.460 ... (remaining 114795 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 83.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.560 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.090 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 : 0.005 0.076 14155 Z= 0.238 Angle : 0.870 13.695 19205 Z= 0.503 Chirality : 0.075 1.231 2185 Planarity : 0.008 0.083 2490 Dihedral : 12.554 78.172 5340 Min Nonbonded Distance : 0.523 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.17), residues: 1745 helix: -0.72 (0.12), residues: 1165 sheet: -2.36 (0.48), residues: 45 loop : 0.86 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.005 TRP J 184 HIS 0.009 0.004 HIS J 12 PHE 0.021 0.003 PHE G 40 TYR 0.026 0.005 TYR G 169 ARG 0.017 0.002 ARG F 167 Details of bonding type rmsd hydrogen bonds : bond 0.12795 ( 860) hydrogen bonds : angle 6.00068 ( 2490) covalent geometry : bond 0.00484 (14155) covalent geometry : angle 0.86960 (19205) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 627 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.8725 (t) cc_final: 0.8298 (p) REVERT: A 41 SER cc_start: 0.8852 (t) cc_final: 0.8565 (m) REVERT: A 66 MET cc_start: 0.8883 (tpt) cc_final: 0.8385 (tpt) REVERT: A 170 LYS cc_start: 0.8291 (tttm) cc_final: 0.7983 (ttmt) REVERT: A 186 THR cc_start: 0.8868 (m) cc_final: 0.8589 (p) REVERT: B 179 GLN cc_start: 0.8543 (tp40) cc_final: 0.8254 (tp-100) REVERT: B 183 ASN cc_start: 0.8717 (m-40) cc_final: 0.8420 (m-40) REVERT: B 210 THR cc_start: 0.8823 (p) cc_final: 0.8584 (p) REVERT: C 216 THR cc_start: 0.9468 (m) cc_final: 0.9153 (p) REVERT: D 41 SER cc_start: 0.8807 (t) cc_final: 0.8527 (m) REVERT: D 170 LYS cc_start: 0.8248 (tttm) cc_final: 0.8019 (tptt) REVERT: D 186 THR cc_start: 0.8871 (m) cc_final: 0.8655 (p) REVERT: E 179 GLN cc_start: 0.8503 (tp40) cc_final: 0.7998 (tp-100) REVERT: E 183 ASN cc_start: 0.8718 (m-40) cc_final: 0.8188 (m-40) REVERT: F 185 MET cc_start: 0.8169 (mtm) cc_final: 0.7919 (mtp) REVERT: F 199 LYS cc_start: 0.8964 (tttm) cc_final: 0.8761 (tttt) REVERT: F 216 THR cc_start: 0.9429 (m) cc_final: 0.9067 (p) REVERT: G 37 ILE cc_start: 0.9094 (mt) cc_final: 0.8885 (mm) REVERT: G 41 SER cc_start: 0.8798 (t) cc_final: 0.8545 (m) REVERT: G 170 LYS cc_start: 0.8346 (tttm) cc_final: 0.8094 (tptt) REVERT: H 192 GLN cc_start: 0.8905 (tp40) cc_final: 0.8661 (tp40) REVERT: I 166 ASP cc_start: 0.8215 (m-30) cc_final: 0.7790 (m-30) REVERT: I 216 THR cc_start: 0.9476 (m) cc_final: 0.9123 (p) REVERT: J 41 SER cc_start: 0.8746 (t) cc_final: 0.8487 (m) REVERT: J 170 LYS cc_start: 0.8305 (tttm) cc_final: 0.7982 (ttmt) REVERT: K 210 THR cc_start: 0.8888 (p) cc_final: 0.8538 (p) REVERT: L 170 LYS cc_start: 0.8448 (tttm) cc_final: 0.8135 (ttpp) REVERT: L 185 MET cc_start: 0.8084 (mtm) cc_final: 0.7765 (mtp) REVERT: L 216 THR cc_start: 0.9448 (m) cc_final: 0.9138 (p) REVERT: M 33 SER cc_start: 0.8623 (t) cc_final: 0.8320 (t) REVERT: M 41 SER cc_start: 0.8717 (t) cc_final: 0.8484 (m) REVERT: M 170 LYS cc_start: 0.8219 (tttm) cc_final: 0.7942 (tptt) REVERT: M 221 VAL cc_start: 0.7806 (p) cc_final: 0.7591 (t) REVERT: N 166 ASP cc_start: 0.8072 (m-30) cc_final: 0.7870 (m-30) REVERT: O 170 LYS cc_start: 0.8507 (tttm) cc_final: 0.8151 (ttpp) REVERT: O 216 THR cc_start: 0.9439 (m) cc_final: 0.9102 (p) outliers start: 0 outliers final: 0 residues processed: 627 average time/residue: 0.3493 time to fit residues: 296.7507 Evaluate side-chains 516 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 516 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 0.2980 chunk 99 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS C 192 GLN F 192 GLN F 219 GLN H 155 GLN H 193 ASN M 219 GLN O 195 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.129057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.103268 restraints weight = 21364.967| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.25 r_work: 0.3077 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14155 Z= 0.159 Angle : 0.624 10.789 19205 Z= 0.315 Chirality : 0.043 0.153 2185 Planarity : 0.005 0.036 2490 Dihedral : 4.744 19.846 1890 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.87 % Allowed : 10.47 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.18), residues: 1745 helix: 0.98 (0.14), residues: 1150 sheet: -2.34 (0.48), residues: 45 loop : 1.21 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 184 HIS 0.002 0.001 HIS G 12 PHE 0.009 0.001 PHE J 40 TYR 0.011 0.001 TYR K 169 ARG 0.007 0.001 ARG N 154 Details of bonding type rmsd hydrogen bonds : bond 0.04314 ( 860) hydrogen bonds : angle 4.33226 ( 2490) covalent geometry : bond 0.00393 (14155) covalent geometry : angle 0.62426 (19205) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 524 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.9152 (tpt) cc_final: 0.8752 (tpt) REVERT: B 200 THR cc_start: 0.8895 (m) cc_final: 0.8565 (p) REVERT: B 202 LEU cc_start: 0.9001 (mt) cc_final: 0.8762 (mt) REVERT: C 170 LYS cc_start: 0.8789 (ttmm) cc_final: 0.8539 (ttpp) REVERT: C 183 ASN cc_start: 0.9368 (m-40) cc_final: 0.9062 (m-40) REVERT: C 197 ASP cc_start: 0.8784 (p0) cc_final: 0.8542 (p0) REVERT: C 201 ILE cc_start: 0.9367 (mt) cc_final: 0.9165 (mp) REVERT: D 128 GLU cc_start: 0.8260 (tp30) cc_final: 0.8042 (tp30) REVERT: D 154 ARG cc_start: 0.8541 (mtt-85) cc_final: 0.8294 (mtt-85) REVERT: D 176 GLN cc_start: 0.6973 (pm20) cc_final: 0.6627 (pm20) REVERT: F 170 LYS cc_start: 0.8856 (ttmm) cc_final: 0.8592 (ttpp) REVERT: F 183 ASN cc_start: 0.9114 (m-40) cc_final: 0.8854 (m-40) REVERT: F 195 ASN cc_start: 0.8195 (m-40) cc_final: 0.7988 (m110) REVERT: G 67 GLN cc_start: 0.8886 (tp40) cc_final: 0.8671 (tp40) REVERT: G 176 GLN cc_start: 0.6885 (pm20) cc_final: 0.6559 (pm20) REVERT: G 192 GLN cc_start: 0.9205 (tp40) cc_final: 0.8854 (tp40) REVERT: H 192 GLN cc_start: 0.9187 (tp40) cc_final: 0.8941 (tp40) REVERT: H 195 ASN cc_start: 0.8447 (t0) cc_final: 0.8145 (t0) REVERT: I 166 ASP cc_start: 0.8633 (m-30) cc_final: 0.8291 (m-30) REVERT: I 170 LYS cc_start: 0.8881 (ttmm) cc_final: 0.8666 (ttpp) REVERT: I 175 GLU cc_start: 0.7702 (tp30) cc_final: 0.7429 (tt0) REVERT: I 183 ASN cc_start: 0.9209 (m-40) cc_final: 0.8927 (m-40) REVERT: J 162 ARG cc_start: 0.8032 (ttt90) cc_final: 0.7768 (ttp80) REVERT: J 192 GLN cc_start: 0.9123 (tp40) cc_final: 0.8781 (tp40) REVERT: K 200 THR cc_start: 0.9009 (m) cc_final: 0.8657 (p) REVERT: L 195 ASN cc_start: 0.8569 (m-40) cc_final: 0.8174 (m110) REVERT: N 200 THR cc_start: 0.8989 (m) cc_final: 0.8648 (p) REVERT: O 183 ASN cc_start: 0.9275 (m-40) cc_final: 0.8995 (m-40) outliers start: 28 outliers final: 13 residues processed: 542 average time/residue: 0.3600 time to fit residues: 266.5562 Evaluate side-chains 499 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 486 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 198 CYS Chi-restraints excluded: chain I residue 152 ASP Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain O residue 205 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 146 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 88 optimal weight: 0.0010 chunk 92 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 GLN B 193 ASN H 155 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.141435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.111605 restraints weight = 22118.331| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.51 r_work: 0.3296 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14155 Z= 0.130 Angle : 0.569 9.913 19205 Z= 0.289 Chirality : 0.042 0.168 2185 Planarity : 0.005 0.041 2490 Dihedral : 4.428 19.831 1890 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.73 % Allowed : 11.93 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.19), residues: 1745 helix: 1.31 (0.14), residues: 1165 sheet: -2.46 (0.48), residues: 45 loop : 1.37 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 184 HIS 0.001 0.001 HIS D 62 PHE 0.008 0.001 PHE G 32 TYR 0.010 0.001 TYR O 169 ARG 0.008 0.001 ARG H 154 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 860) hydrogen bonds : angle 4.11938 ( 2490) covalent geometry : bond 0.00309 (14155) covalent geometry : angle 0.56856 (19205) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 496 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8636 (tt0) cc_final: 0.8355 (tt0) REVERT: A 66 MET cc_start: 0.9058 (tpt) cc_final: 0.8531 (tpt) REVERT: A 67 GLN cc_start: 0.8704 (tp40) cc_final: 0.8441 (tp40) REVERT: A 113 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7799 (mt-10) REVERT: A 170 LYS cc_start: 0.8460 (tptt) cc_final: 0.8251 (mmtt) REVERT: A 176 GLN cc_start: 0.6273 (pm20) cc_final: 0.5964 (pm20) REVERT: A 192 GLN cc_start: 0.8991 (tp40) cc_final: 0.8630 (tm-30) REVERT: A 198 CYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7990 (m) REVERT: C 159 GLU cc_start: 0.8487 (tt0) cc_final: 0.8233 (tt0) REVERT: C 167 ARG cc_start: 0.9153 (mtp-110) cc_final: 0.8661 (mtm110) REVERT: C 170 LYS cc_start: 0.8663 (ttmm) cc_final: 0.8402 (ttpp) REVERT: C 183 ASN cc_start: 0.8980 (m-40) cc_final: 0.8660 (m-40) REVERT: C 192 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8096 (mp-120) REVERT: D 162 ARG cc_start: 0.8218 (ttp-170) cc_final: 0.8008 (ttt-90) REVERT: E 213 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8383 (mt-10) REVERT: F 170 LYS cc_start: 0.8673 (ttmm) cc_final: 0.8388 (ttpp) REVERT: F 183 ASN cc_start: 0.8967 (m-40) cc_final: 0.8709 (m-40) REVERT: F 195 ASN cc_start: 0.8091 (m-40) cc_final: 0.7853 (m110) REVERT: F 213 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8279 (mt-10) REVERT: I 170 LYS cc_start: 0.8720 (ttmm) cc_final: 0.8504 (ttpp) REVERT: I 175 GLU cc_start: 0.7707 (tp30) cc_final: 0.7424 (mt-10) REVERT: I 183 ASN cc_start: 0.9000 (m-40) cc_final: 0.8751 (m-40) REVERT: I 185 MET cc_start: 0.8033 (mtt) cc_final: 0.7778 (mtt) REVERT: J 176 GLN cc_start: 0.6456 (pm20) cc_final: 0.6091 (pm20) REVERT: J 192 GLN cc_start: 0.9010 (tp40) cc_final: 0.8706 (tp40) REVERT: K 200 THR cc_start: 0.8931 (m) cc_final: 0.8616 (p) REVERT: L 195 ASN cc_start: 0.8343 (m-40) cc_final: 0.7841 (m110) REVERT: L 213 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8070 (mt-10) REVERT: M 67 GLN cc_start: 0.8687 (tp40) cc_final: 0.8435 (tp40) REVERT: M 113 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7711 (mt-10) REVERT: M 176 GLN cc_start: 0.6806 (pm20) cc_final: 0.6451 (pm20) REVERT: M 192 GLN cc_start: 0.9053 (tp40) cc_final: 0.8723 (tp40) REVERT: M 203 LYS cc_start: 0.9064 (mmtp) cc_final: 0.8849 (mmtp) REVERT: N 200 THR cc_start: 0.8949 (m) cc_final: 0.8576 (p) REVERT: O 183 ASN cc_start: 0.9002 (m-40) cc_final: 0.8725 (m-40) REVERT: O 213 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8102 (mt-10) outliers start: 26 outliers final: 10 residues processed: 508 average time/residue: 0.3805 time to fit residues: 263.3340 Evaluate side-chains 475 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 463 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain C residue 192 GLN Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain G residue 198 CYS Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 218 CYS Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain O residue 212 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 22 optimal weight: 1.9990 chunk 91 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 150 optimal weight: 0.0770 chunk 56 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 GLN C 195 ASN D 50 GLN H 179 GLN J 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.128606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.102144 restraints weight = 21440.555| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.28 r_work: 0.3087 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14155 Z= 0.151 Angle : 0.581 10.353 19205 Z= 0.292 Chirality : 0.043 0.185 2185 Planarity : 0.005 0.038 2490 Dihedral : 4.327 17.937 1890 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.13 % Allowed : 13.60 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.19), residues: 1745 helix: 1.23 (0.15), residues: 1175 sheet: -2.37 (0.49), residues: 45 loop : 1.22 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 184 HIS 0.001 0.000 HIS A 12 PHE 0.010 0.001 PHE M 32 TYR 0.011 0.001 TYR K 169 ARG 0.006 0.001 ARG H 154 Details of bonding type rmsd hydrogen bonds : bond 0.03808 ( 860) hydrogen bonds : angle 4.09388 ( 2490) covalent geometry : bond 0.00369 (14155) covalent geometry : angle 0.58052 (19205) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 491 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.9083 (tpt) cc_final: 0.8622 (tpt) REVERT: A 67 GLN cc_start: 0.8824 (tp40) cc_final: 0.8587 (tp40) REVERT: A 113 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7930 (mt-10) REVERT: A 162 ARG cc_start: 0.8372 (ttp80) cc_final: 0.8102 (ttp80) REVERT: A 192 GLN cc_start: 0.9171 (tp40) cc_final: 0.8867 (tm-30) REVERT: A 198 CYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8095 (m) REVERT: B 200 THR cc_start: 0.8992 (m) cc_final: 0.8665 (p) REVERT: C 170 LYS cc_start: 0.8766 (ttmm) cc_final: 0.8513 (ttpp) REVERT: C 179 GLN cc_start: 0.8924 (tp40) cc_final: 0.8558 (tp-100) REVERT: C 183 ASN cc_start: 0.9052 (m-40) cc_final: 0.8508 (m-40) REVERT: D 113 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7914 (mt-10) REVERT: D 176 GLN cc_start: 0.6598 (pm20) cc_final: 0.6075 (pm20) REVERT: E 192 GLN cc_start: 0.9078 (tp40) cc_final: 0.8782 (tp40) REVERT: F 170 LYS cc_start: 0.8765 (ttmm) cc_final: 0.8488 (ttpp) REVERT: F 195 ASN cc_start: 0.8151 (m-40) cc_final: 0.7877 (m110) REVERT: G 67 GLN cc_start: 0.8782 (tp40) cc_final: 0.8530 (tp40) REVERT: G 176 GLN cc_start: 0.6377 (pm20) cc_final: 0.6171 (pm20) REVERT: G 192 GLN cc_start: 0.9091 (tp40) cc_final: 0.8863 (tp40) REVERT: H 197 ASP cc_start: 0.8456 (p0) cc_final: 0.8207 (p0) REVERT: H 200 THR cc_start: 0.8950 (m) cc_final: 0.8616 (p) REVERT: I 170 LYS cc_start: 0.8842 (ttmm) cc_final: 0.8582 (ttpp) REVERT: I 175 GLU cc_start: 0.7823 (tp30) cc_final: 0.7325 (mt-10) REVERT: I 183 ASN cc_start: 0.9133 (m-40) cc_final: 0.8880 (m-40) REVERT: I 185 MET cc_start: 0.8084 (mtt) cc_final: 0.7854 (mtt) REVERT: J 67 GLN cc_start: 0.8710 (tp40) cc_final: 0.8465 (tp40) REVERT: J 176 GLN cc_start: 0.6647 (pm20) cc_final: 0.6345 (pm20) REVERT: J 192 GLN cc_start: 0.9169 (tp40) cc_final: 0.8903 (tp40) REVERT: K 200 THR cc_start: 0.9017 (m) cc_final: 0.8697 (p) REVERT: L 195 ASN cc_start: 0.8468 (m-40) cc_final: 0.8007 (m110) REVERT: L 213 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8323 (mt-10) REVERT: M 13 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7820 (tt0) REVERT: M 67 GLN cc_start: 0.8835 (tp40) cc_final: 0.8614 (tp40) REVERT: M 113 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7917 (mt-10) REVERT: M 176 GLN cc_start: 0.6992 (pm20) cc_final: 0.6683 (pm20) REVERT: M 192 GLN cc_start: 0.9182 (tp40) cc_final: 0.8944 (tp40) REVERT: N 200 THR cc_start: 0.8949 (m) cc_final: 0.8614 (p) REVERT: O 183 ASN cc_start: 0.9132 (m-40) cc_final: 0.8906 (m-40) REVERT: O 203 LYS cc_start: 0.8310 (mmtp) cc_final: 0.8093 (mttm) outliers start: 32 outliers final: 16 residues processed: 506 average time/residue: 0.3243 time to fit residues: 222.7402 Evaluate side-chains 475 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 458 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain D residue 120 HIS Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 198 CYS Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 218 CYS Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 120 HIS Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 210 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 66 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 124 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 138 optimal weight: 0.3980 chunk 85 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN B 179 GLN C 195 ASN D 50 GLN G 50 GLN H 179 GLN H 193 ASN J 50 GLN M 50 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.140872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.110719 restraints weight = 22146.873| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.53 r_work: 0.3288 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14155 Z= 0.126 Angle : 0.557 9.861 19205 Z= 0.281 Chirality : 0.041 0.159 2185 Planarity : 0.005 0.040 2490 Dihedral : 4.190 17.426 1890 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.53 % Allowed : 14.40 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.19), residues: 1745 helix: 1.30 (0.15), residues: 1165 sheet: -2.34 (0.50), residues: 45 loop : 1.39 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 184 HIS 0.001 0.000 HIS G 12 PHE 0.008 0.001 PHE L 168 TYR 0.011 0.001 TYR M 145 ARG 0.009 0.000 ARG H 154 Details of bonding type rmsd hydrogen bonds : bond 0.03590 ( 860) hydrogen bonds : angle 4.01646 ( 2490) covalent geometry : bond 0.00301 (14155) covalent geometry : angle 0.55724 (19205) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 465 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.9027 (tpt) cc_final: 0.8531 (tpt) REVERT: A 113 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7849 (mt-10) REVERT: A 162 ARG cc_start: 0.8235 (ttp80) cc_final: 0.7956 (ttp80) REVERT: A 198 CYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7931 (m) REVERT: B 200 THR cc_start: 0.8886 (m) cc_final: 0.8584 (p) REVERT: C 159 GLU cc_start: 0.8504 (tt0) cc_final: 0.8206 (tt0) REVERT: C 167 ARG cc_start: 0.9120 (mtp180) cc_final: 0.8914 (mtm110) REVERT: C 170 LYS cc_start: 0.8645 (ttmm) cc_final: 0.8384 (ttpp) REVERT: C 179 GLN cc_start: 0.8857 (tp40) cc_final: 0.8655 (tp40) REVERT: C 183 ASN cc_start: 0.8887 (m-40) cc_final: 0.8469 (m-40) REVERT: D 68 MET cc_start: 0.8338 (mtp) cc_final: 0.7970 (mtp) REVERT: D 113 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7811 (mt-10) REVERT: D 176 GLN cc_start: 0.6298 (pm20) cc_final: 0.6029 (pm20) REVERT: E 192 GLN cc_start: 0.9004 (tp40) cc_final: 0.8729 (tp40) REVERT: F 170 LYS cc_start: 0.8651 (ttmm) cc_final: 0.8348 (ttpp) REVERT: F 182 LYS cc_start: 0.8653 (mttm) cc_final: 0.8441 (mttp) REVERT: F 195 ASN cc_start: 0.8231 (m-40) cc_final: 0.7968 (m110) REVERT: H 197 ASP cc_start: 0.8311 (p0) cc_final: 0.8008 (p0) REVERT: H 200 THR cc_start: 0.8923 (m) cc_final: 0.8614 (p) REVERT: I 170 LYS cc_start: 0.8736 (ttmm) cc_final: 0.8476 (ttpp) REVERT: I 175 GLU cc_start: 0.7797 (tp30) cc_final: 0.7206 (mt-10) REVERT: K 154 ARG cc_start: 0.8378 (mtt-85) cc_final: 0.8148 (mmt-90) REVERT: K 200 THR cc_start: 0.8977 (m) cc_final: 0.8676 (p) REVERT: L 179 GLN cc_start: 0.8891 (tp40) cc_final: 0.8529 (tp40) REVERT: L 195 ASN cc_start: 0.8449 (m-40) cc_final: 0.7961 (m110) REVERT: L 213 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8093 (mt-10) REVERT: M 13 GLN cc_start: 0.8126 (tm-30) cc_final: 0.7708 (tt0) REVERT: M 67 GLN cc_start: 0.8694 (tp40) cc_final: 0.8387 (tp40) REVERT: M 113 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7838 (mt-10) REVERT: M 175 GLU cc_start: 0.6941 (mm-30) cc_final: 0.6714 (mm-30) REVERT: M 176 GLN cc_start: 0.6704 (pm20) cc_final: 0.6489 (pm20) REVERT: M 192 GLN cc_start: 0.9008 (tp40) cc_final: 0.8778 (tp40) REVERT: N 200 THR cc_start: 0.8915 (m) cc_final: 0.8584 (p) REVERT: O 183 ASN cc_start: 0.8981 (m-40) cc_final: 0.8547 (m-40) REVERT: O 203 LYS cc_start: 0.8315 (mmtp) cc_final: 0.8115 (mttm) outliers start: 23 outliers final: 17 residues processed: 473 average time/residue: 0.3309 time to fit residues: 212.2377 Evaluate side-chains 481 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 463 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain D residue 120 HIS Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain G residue 198 CYS Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 218 CYS Chi-restraints excluded: chain M residue 120 HIS Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain O residue 159 GLU Chi-restraints excluded: chain O residue 212 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 0 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 161 optimal weight: 0.3980 chunk 9 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 GLN C 155 GLN D 50 GLN H 179 GLN M 50 GLN O 155 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.139321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.108376 restraints weight = 22047.021| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.56 r_work: 0.3245 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14155 Z= 0.145 Angle : 0.573 9.953 19205 Z= 0.290 Chirality : 0.042 0.167 2185 Planarity : 0.005 0.039 2490 Dihedral : 4.201 17.631 1890 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.80 % Allowed : 14.93 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.19), residues: 1745 helix: 1.21 (0.15), residues: 1170 sheet: -2.39 (0.47), residues: 45 loop : 1.36 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 184 HIS 0.002 0.000 HIS G 12 PHE 0.009 0.001 PHE M 32 TYR 0.013 0.001 TYR O 169 ARG 0.006 0.000 ARG H 154 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 860) hydrogen bonds : angle 4.04004 ( 2490) covalent geometry : bond 0.00356 (14155) covalent geometry : angle 0.57250 (19205) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 475 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.9029 (tpt) cc_final: 0.8516 (tpt) REVERT: A 67 GLN cc_start: 0.8685 (tp40) cc_final: 0.8424 (tp40) REVERT: A 145 TYR cc_start: 0.8719 (m-80) cc_final: 0.8418 (m-80) REVERT: A 162 ARG cc_start: 0.8274 (ttp80) cc_final: 0.7982 (ttp80) REVERT: A 176 GLN cc_start: 0.6167 (pm20) cc_final: 0.5823 (pm20) REVERT: A 192 GLN cc_start: 0.9050 (tp40) cc_final: 0.8717 (tm-30) REVERT: A 198 CYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7980 (m) REVERT: B 200 THR cc_start: 0.8866 (m) cc_final: 0.8545 (p) REVERT: B 203 LYS cc_start: 0.8870 (mtpp) cc_final: 0.8528 (mtmt) REVERT: C 167 ARG cc_start: 0.9133 (mtp180) cc_final: 0.8873 (mtm110) REVERT: C 170 LYS cc_start: 0.8648 (ttmm) cc_final: 0.8371 (ttpp) REVERT: C 179 GLN cc_start: 0.8856 (tp40) cc_final: 0.8648 (tp40) REVERT: C 183 ASN cc_start: 0.8882 (m-40) cc_final: 0.8423 (m-40) REVERT: C 199 LYS cc_start: 0.8972 (ttpp) cc_final: 0.8763 (ttpt) REVERT: D 68 MET cc_start: 0.8386 (mtp) cc_final: 0.7985 (mtp) REVERT: D 113 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7826 (mt-10) REVERT: D 176 GLN cc_start: 0.6132 (pm20) cc_final: 0.5908 (pm20) REVERT: E 192 GLN cc_start: 0.8996 (tp40) cc_final: 0.8733 (tp40) REVERT: E 213 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8538 (mp0) REVERT: F 170 LYS cc_start: 0.8683 (ttmm) cc_final: 0.8376 (ttpp) REVERT: F 182 LYS cc_start: 0.8671 (mttm) cc_final: 0.8465 (mttp) REVERT: F 195 ASN cc_start: 0.8250 (m-40) cc_final: 0.7974 (m110) REVERT: F 213 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8772 (pm20) REVERT: G 67 GLN cc_start: 0.8586 (tp40) cc_final: 0.8354 (tp40) REVERT: G 176 GLN cc_start: 0.5859 (pm20) cc_final: 0.5512 (pm20) REVERT: G 192 GLN cc_start: 0.8978 (tp40) cc_final: 0.8738 (tp40) REVERT: H 197 ASP cc_start: 0.8255 (p0) cc_final: 0.7972 (p0) REVERT: H 200 THR cc_start: 0.8986 (m) cc_final: 0.8696 (p) REVERT: I 166 ASP cc_start: 0.8416 (m-30) cc_final: 0.8209 (m-30) REVERT: I 170 LYS cc_start: 0.8691 (ttmm) cc_final: 0.8419 (ttpp) REVERT: I 175 GLU cc_start: 0.7708 (tp30) cc_final: 0.7153 (mt-10) REVERT: J 67 GLN cc_start: 0.8635 (tp40) cc_final: 0.8330 (tp40) REVERT: J 176 GLN cc_start: 0.6400 (pm20) cc_final: 0.5800 (pm20) REVERT: J 192 GLN cc_start: 0.9056 (tp40) cc_final: 0.8764 (tp40) REVERT: K 200 THR cc_start: 0.8955 (m) cc_final: 0.8666 (p) REVERT: L 195 ASN cc_start: 0.8418 (m-40) cc_final: 0.7910 (m110) REVERT: L 213 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8113 (mt-10) REVERT: M 67 GLN cc_start: 0.8696 (tp40) cc_final: 0.8378 (tp40) REVERT: M 175 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6714 (mm-30) REVERT: N 200 THR cc_start: 0.8971 (m) cc_final: 0.8615 (p) REVERT: N 213 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8550 (mt-10) REVERT: O 179 GLN cc_start: 0.8963 (tp40) cc_final: 0.8517 (tp40) REVERT: O 183 ASN cc_start: 0.9024 (m-40) cc_final: 0.8678 (m-40) outliers start: 27 outliers final: 21 residues processed: 484 average time/residue: 0.3252 time to fit residues: 212.0787 Evaluate side-chains 490 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 467 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain D residue 120 HIS Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 213 GLU Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain G residue 198 CYS Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 120 HIS Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 150 ILE Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain O residue 159 GLU Chi-restraints excluded: chain O residue 212 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 22 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 164 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 150 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN B 179 GLN D 50 GLN ** F 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 GLN I 183 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.139025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.107957 restraints weight = 22073.579| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.56 r_work: 0.3251 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14155 Z= 0.144 Angle : 0.582 10.509 19205 Z= 0.294 Chirality : 0.042 0.169 2185 Planarity : 0.005 0.040 2490 Dihedral : 4.190 17.599 1890 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.07 % Allowed : 15.00 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.19), residues: 1745 helix: 1.11 (0.15), residues: 1180 sheet: -2.45 (0.47), residues: 45 loop : 1.23 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 184 HIS 0.001 0.000 HIS G 12 PHE 0.009 0.001 PHE G 32 TYR 0.021 0.001 TYR O 164 ARG 0.008 0.000 ARG H 154 Details of bonding type rmsd hydrogen bonds : bond 0.03682 ( 860) hydrogen bonds : angle 4.05667 ( 2490) covalent geometry : bond 0.00354 (14155) covalent geometry : angle 0.58235 (19205) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 476 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8249 (mtm180) REVERT: A 66 MET cc_start: 0.9022 (tpt) cc_final: 0.8504 (tpt) REVERT: A 67 GLN cc_start: 0.8698 (tp40) cc_final: 0.8445 (tp40) REVERT: A 176 GLN cc_start: 0.6116 (pm20) cc_final: 0.5805 (pm20) REVERT: A 192 GLN cc_start: 0.9057 (tp40) cc_final: 0.8723 (tm-30) REVERT: A 198 CYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7969 (m) REVERT: B 200 THR cc_start: 0.8856 (m) cc_final: 0.8538 (p) REVERT: B 203 LYS cc_start: 0.8900 (mtpp) cc_final: 0.8564 (mtmt) REVERT: C 167 ARG cc_start: 0.9128 (mtp180) cc_final: 0.8911 (mtp180) REVERT: C 170 LYS cc_start: 0.8639 (ttmm) cc_final: 0.8361 (ttpp) REVERT: C 179 GLN cc_start: 0.8876 (tp40) cc_final: 0.8666 (tp40) REVERT: C 183 ASN cc_start: 0.8847 (m-40) cc_final: 0.8445 (m-40) REVERT: D 113 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7826 (mt-10) REVERT: E 192 GLN cc_start: 0.8989 (tp40) cc_final: 0.8727 (tp40) REVERT: F 170 LYS cc_start: 0.8687 (ttmm) cc_final: 0.8385 (ttpp) REVERT: F 195 ASN cc_start: 0.8312 (m-40) cc_final: 0.8029 (m110) REVERT: G 67 GLN cc_start: 0.8693 (tp40) cc_final: 0.8449 (tp40) REVERT: G 176 GLN cc_start: 0.5786 (pm20) cc_final: 0.5385 (pm20) REVERT: G 192 GLN cc_start: 0.8987 (tp40) cc_final: 0.8748 (tp40) REVERT: H 179 GLN cc_start: 0.8680 (tp40) cc_final: 0.8460 (tp-100) REVERT: H 197 ASP cc_start: 0.8224 (p0) cc_final: 0.7988 (p0) REVERT: H 200 THR cc_start: 0.8988 (m) cc_final: 0.8706 (p) REVERT: H 213 GLU cc_start: 0.8772 (mp0) cc_final: 0.8540 (pm20) REVERT: I 166 ASP cc_start: 0.8429 (m-30) cc_final: 0.7996 (m-30) REVERT: I 170 LYS cc_start: 0.8695 (ttmm) cc_final: 0.8417 (ttpp) REVERT: I 175 GLU cc_start: 0.7683 (tp30) cc_final: 0.7181 (mt-10) REVERT: J 67 GLN cc_start: 0.8668 (tp40) cc_final: 0.8357 (tp40) REVERT: J 176 GLN cc_start: 0.6397 (pm20) cc_final: 0.5832 (pm20) REVERT: J 192 GLN cc_start: 0.9050 (tp40) cc_final: 0.8757 (tp40) REVERT: K 200 THR cc_start: 0.8956 (m) cc_final: 0.8677 (p) REVERT: L 175 GLU cc_start: 0.7900 (tt0) cc_final: 0.7517 (mt-10) REVERT: L 195 ASN cc_start: 0.8411 (m-40) cc_final: 0.7901 (m110) REVERT: L 213 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8094 (mt-10) REVERT: M 67 GLN cc_start: 0.8715 (tp40) cc_final: 0.8466 (tp40) REVERT: M 176 GLN cc_start: 0.6153 (pm20) cc_final: 0.5586 (pm20) REVERT: M 192 GLN cc_start: 0.9011 (tp40) cc_final: 0.8792 (tp40) REVERT: N 154 ARG cc_start: 0.8604 (mtt-85) cc_final: 0.8357 (mmt-90) REVERT: N 200 THR cc_start: 0.8927 (m) cc_final: 0.8607 (p) REVERT: N 213 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8555 (mt-10) REVERT: O 179 GLN cc_start: 0.8980 (tp40) cc_final: 0.8477 (tp40) REVERT: O 183 ASN cc_start: 0.8941 (m-40) cc_final: 0.8441 (m-40) outliers start: 31 outliers final: 22 residues processed: 489 average time/residue: 0.3232 time to fit residues: 213.9620 Evaluate side-chains 490 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 466 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain D residue 120 HIS Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain G residue 198 CYS Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 218 CYS Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 120 HIS Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain O residue 159 GLU Chi-restraints excluded: chain O residue 212 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 113 optimal weight: 0.5980 chunk 141 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 134 optimal weight: 0.0980 chunk 131 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 138 optimal weight: 0.5980 chunk 136 optimal weight: 0.0170 chunk 52 optimal weight: 7.9990 chunk 140 optimal weight: 0.7980 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 GLN F 179 GLN F 183 ASN G 50 GLN I 179 GLN N 193 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.135888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.106065 restraints weight = 21385.682| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.39 r_work: 0.3225 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14155 Z= 0.110 Angle : 0.553 9.315 19205 Z= 0.281 Chirality : 0.041 0.159 2185 Planarity : 0.005 0.041 2490 Dihedral : 4.027 16.480 1890 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.67 % Allowed : 15.93 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.19), residues: 1745 helix: 1.20 (0.15), residues: 1180 sheet: -2.36 (0.49), residues: 45 loop : 1.27 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 184 HIS 0.001 0.000 HIS M 62 PHE 0.008 0.001 PHE E 168 TYR 0.013 0.001 TYR G 145 ARG 0.006 0.001 ARG M 132 Details of bonding type rmsd hydrogen bonds : bond 0.03394 ( 860) hydrogen bonds : angle 3.96992 ( 2490) covalent geometry : bond 0.00255 (14155) covalent geometry : angle 0.55307 (19205) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 473 time to evaluate : 2.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.9046 (tpt) cc_final: 0.8658 (tpt) REVERT: A 67 GLN cc_start: 0.8795 (tp40) cc_final: 0.8548 (tp40) REVERT: A 176 GLN cc_start: 0.5988 (pm20) cc_final: 0.5458 (pm20) REVERT: A 192 GLN cc_start: 0.9148 (tp40) cc_final: 0.8834 (tm-30) REVERT: A 198 CYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7948 (m) REVERT: B 179 GLN cc_start: 0.8660 (tp40) cc_final: 0.8138 (tp-100) REVERT: B 183 ASN cc_start: 0.9038 (m-40) cc_final: 0.8542 (m-40) REVERT: B 200 THR cc_start: 0.8906 (m) cc_final: 0.8627 (p) REVERT: B 203 LYS cc_start: 0.8856 (mtpp) cc_final: 0.8531 (mtmt) REVERT: B 213 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8735 (mp0) REVERT: C 167 ARG cc_start: 0.9080 (mtp180) cc_final: 0.8849 (mtm110) REVERT: C 170 LYS cc_start: 0.8702 (ttmm) cc_final: 0.8429 (ttpp) REVERT: C 179 GLN cc_start: 0.8888 (tp40) cc_final: 0.8637 (tp40) REVERT: C 183 ASN cc_start: 0.8910 (m-40) cc_final: 0.8523 (m-40) REVERT: D 113 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7939 (mt-10) REVERT: D 176 GLN cc_start: 0.5656 (pm20) cc_final: 0.4989 (pm20) REVERT: E 192 GLN cc_start: 0.9093 (tp40) cc_final: 0.8865 (tp40) REVERT: E 200 THR cc_start: 0.8927 (m) cc_final: 0.8675 (p) REVERT: F 170 LYS cc_start: 0.8752 (ttmm) cc_final: 0.8472 (ttpp) REVERT: F 195 ASN cc_start: 0.8339 (m-40) cc_final: 0.8043 (m110) REVERT: F 213 GLU cc_start: 0.9125 (pm20) cc_final: 0.8898 (pm20) REVERT: G 53 ASN cc_start: 0.8720 (m-40) cc_final: 0.8514 (m-40) REVERT: G 67 GLN cc_start: 0.8835 (tp40) cc_final: 0.8557 (tp40) REVERT: G 176 GLN cc_start: 0.5719 (pm20) cc_final: 0.5178 (pm20) REVERT: H 154 ARG cc_start: 0.8363 (mtt90) cc_final: 0.8106 (mmt-90) REVERT: H 197 ASP cc_start: 0.8238 (p0) cc_final: 0.7946 (p0) REVERT: H 200 THR cc_start: 0.8988 (m) cc_final: 0.8705 (p) REVERT: I 170 LYS cc_start: 0.8751 (ttmm) cc_final: 0.8475 (ttpp) REVERT: I 175 GLU cc_start: 0.7655 (tp30) cc_final: 0.7233 (mt-10) REVERT: J 176 GLN cc_start: 0.6432 (pm20) cc_final: 0.5868 (pm20) REVERT: J 192 GLN cc_start: 0.9140 (tp40) cc_final: 0.8810 (tm-30) REVERT: K 200 THR cc_start: 0.8986 (m) cc_final: 0.8690 (p) REVERT: L 195 ASN cc_start: 0.8414 (m-40) cc_final: 0.7998 (m110) REVERT: L 213 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8226 (mt-10) REVERT: M 67 GLN cc_start: 0.8806 (tp40) cc_final: 0.8544 (tp40) REVERT: M 154 ARG cc_start: 0.8949 (mtt90) cc_final: 0.8698 (mtt90) REVERT: M 176 GLN cc_start: 0.6098 (pm20) cc_final: 0.5806 (pm20) REVERT: M 192 GLN cc_start: 0.9092 (tp40) cc_final: 0.8799 (tm-30) REVERT: N 154 ARG cc_start: 0.8671 (mtt-85) cc_final: 0.8448 (mmt-90) REVERT: N 200 THR cc_start: 0.8939 (m) cc_final: 0.8593 (p) REVERT: N 213 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8598 (mt-10) REVERT: N 219 GLN cc_start: 0.8968 (tp40) cc_final: 0.8731 (tp40) REVERT: O 175 GLU cc_start: 0.7748 (tp30) cc_final: 0.7476 (tt0) REVERT: O 212 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8263 (pm20) outliers start: 25 outliers final: 16 residues processed: 485 average time/residue: 0.3454 time to fit residues: 226.2938 Evaluate side-chains 468 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 450 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain C residue 192 GLN Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain D residue 120 HIS Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain G residue 198 CYS Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 218 CYS Chi-restraints excluded: chain M residue 120 HIS Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain O residue 159 GLU Chi-restraints excluded: chain O residue 212 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 104 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 163 optimal weight: 7.9990 chunk 3 optimal weight: 0.0030 chunk 75 optimal weight: 0.7980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 50 GLN I 179 GLN I 183 ASN K 179 GLN M 50 GLN O 179 GLN O 183 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.133561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.103124 restraints weight = 21527.497| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.40 r_work: 0.3184 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14155 Z= 0.130 Angle : 0.591 10.311 19205 Z= 0.298 Chirality : 0.042 0.162 2185 Planarity : 0.005 0.041 2490 Dihedral : 4.078 19.001 1890 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.60 % Allowed : 16.67 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.19), residues: 1745 helix: 1.17 (0.15), residues: 1180 sheet: -2.37 (0.48), residues: 45 loop : 1.22 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 184 HIS 0.001 0.000 HIS G 12 PHE 0.008 0.001 PHE G 32 TYR 0.010 0.001 TYR O 164 ARG 0.007 0.001 ARG E 154 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 860) hydrogen bonds : angle 4.02717 ( 2490) covalent geometry : bond 0.00320 (14155) covalent geometry : angle 0.59105 (19205) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 467 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8703 (tt0) cc_final: 0.8458 (tt0) REVERT: A 66 MET cc_start: 0.9056 (tpt) cc_final: 0.8652 (tpt) REVERT: A 67 GLN cc_start: 0.8815 (tp40) cc_final: 0.8568 (tp40) REVERT: A 176 GLN cc_start: 0.6099 (pm20) cc_final: 0.5595 (pm20) REVERT: A 192 GLN cc_start: 0.9161 (tp40) cc_final: 0.8829 (tm-30) REVERT: A 198 CYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7945 (m) REVERT: B 179 GLN cc_start: 0.8704 (tp40) cc_final: 0.7969 (tp-100) REVERT: B 183 ASN cc_start: 0.9044 (m-40) cc_final: 0.8433 (m-40) REVERT: B 200 THR cc_start: 0.8924 (m) cc_final: 0.8655 (p) REVERT: B 203 LYS cc_start: 0.8854 (mtpp) cc_final: 0.8565 (mtmt) REVERT: C 170 LYS cc_start: 0.8706 (ttmm) cc_final: 0.8443 (ttpp) REVERT: C 179 GLN cc_start: 0.8899 (tp40) cc_final: 0.8626 (tp40) REVERT: C 183 ASN cc_start: 0.8908 (m-40) cc_final: 0.8467 (m-40) REVERT: D 113 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7951 (mt-10) REVERT: D 176 GLN cc_start: 0.5783 (pm20) cc_final: 0.5139 (pm20) REVERT: E 192 GLN cc_start: 0.9088 (tp40) cc_final: 0.8848 (tp40) REVERT: E 200 THR cc_start: 0.8923 (m) cc_final: 0.8702 (p) REVERT: F 170 LYS cc_start: 0.8806 (ttmm) cc_final: 0.8528 (ttpp) REVERT: F 195 ASN cc_start: 0.8347 (m-40) cc_final: 0.8040 (m110) REVERT: G 67 GLN cc_start: 0.8851 (tp40) cc_final: 0.8575 (tp40) REVERT: G 176 GLN cc_start: 0.5851 (pm20) cc_final: 0.5595 (pm20) REVERT: G 192 GLN cc_start: 0.9033 (tp40) cc_final: 0.8514 (tm-30) REVERT: H 154 ARG cc_start: 0.8436 (mtt90) cc_final: 0.8052 (mmt-90) REVERT: H 197 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7910 (p0) REVERT: H 200 THR cc_start: 0.8884 (m) cc_final: 0.8586 (p) REVERT: I 170 LYS cc_start: 0.8772 (ttmm) cc_final: 0.8499 (ttpp) REVERT: I 175 GLU cc_start: 0.7691 (tp30) cc_final: 0.7289 (mt-10) REVERT: J 67 GLN cc_start: 0.8745 (tp40) cc_final: 0.8469 (tp40) REVERT: J 176 GLN cc_start: 0.6486 (pm20) cc_final: 0.5926 (pm20) REVERT: J 192 GLN cc_start: 0.9161 (tp40) cc_final: 0.8828 (tm-30) REVERT: K 154 ARG cc_start: 0.8465 (mmt-90) cc_final: 0.8226 (mmt-90) REVERT: K 200 THR cc_start: 0.9028 (m) cc_final: 0.8739 (p) REVERT: L 195 ASN cc_start: 0.8411 (m-40) cc_final: 0.8017 (m110) REVERT: M 67 GLN cc_start: 0.8842 (tp40) cc_final: 0.8581 (tp40) REVERT: M 68 MET cc_start: 0.8539 (mtp) cc_final: 0.8295 (mtp) REVERT: M 154 ARG cc_start: 0.8986 (mtt90) cc_final: 0.8749 (mtt90) REVERT: M 176 GLN cc_start: 0.6105 (pm20) cc_final: 0.5816 (pm20) REVERT: M 192 GLN cc_start: 0.9097 (tp40) cc_final: 0.8794 (tm-30) REVERT: N 154 ARG cc_start: 0.8727 (mtt-85) cc_final: 0.8514 (mmt-90) REVERT: N 200 THR cc_start: 0.8917 (m) cc_final: 0.8619 (p) REVERT: N 213 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8589 (mt-10) REVERT: N 219 GLN cc_start: 0.8992 (tp40) cc_final: 0.8773 (tp40) REVERT: O 203 LYS cc_start: 0.8297 (mmtp) cc_final: 0.8042 (mttm) REVERT: O 212 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8320 (pm20) outliers start: 24 outliers final: 17 residues processed: 474 average time/residue: 0.3092 time to fit residues: 198.6688 Evaluate side-chains 476 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 456 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain C residue 192 GLN Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain D residue 120 HIS Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain G residue 198 CYS Chi-restraints excluded: chain H residue 197 ASP Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 218 CYS Chi-restraints excluded: chain M residue 120 HIS Chi-restraints excluded: chain N residue 150 ILE Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain O residue 159 GLU Chi-restraints excluded: chain O residue 212 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 GLN E 179 GLN F 219 GLN I 183 ASN O 219 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.132631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.101957 restraints weight = 21598.805| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.41 r_work: 0.3173 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14155 Z= 0.144 Angle : 0.616 12.301 19205 Z= 0.310 Chirality : 0.042 0.158 2185 Planarity : 0.005 0.041 2490 Dihedral : 4.158 17.713 1890 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.53 % Allowed : 16.87 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.19), residues: 1745 helix: 1.07 (0.15), residues: 1180 sheet: -2.32 (0.46), residues: 45 loop : 1.24 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 184 HIS 0.001 0.000 HIS G 12 PHE 0.009 0.001 PHE G 32 TYR 0.016 0.001 TYR F 164 ARG 0.007 0.001 ARG M 132 Details of bonding type rmsd hydrogen bonds : bond 0.03699 ( 860) hydrogen bonds : angle 4.10025 ( 2490) covalent geometry : bond 0.00359 (14155) covalent geometry : angle 0.61630 (19205) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 464 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.9063 (tpt) cc_final: 0.8673 (tpt) REVERT: A 67 GLN cc_start: 0.8806 (tp40) cc_final: 0.8536 (tp40) REVERT: A 145 TYR cc_start: 0.8799 (m-80) cc_final: 0.8525 (m-80) REVERT: A 176 GLN cc_start: 0.6149 (pm20) cc_final: 0.5641 (pm20) REVERT: A 192 GLN cc_start: 0.9132 (tp40) cc_final: 0.8803 (tm-30) REVERT: A 198 CYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7948 (m) REVERT: B 179 GLN cc_start: 0.8675 (tp40) cc_final: 0.8185 (tp-100) REVERT: B 183 ASN cc_start: 0.9040 (m-40) cc_final: 0.8551 (m-40) REVERT: B 200 THR cc_start: 0.8943 (m) cc_final: 0.8680 (p) REVERT: B 203 LYS cc_start: 0.8858 (mtpp) cc_final: 0.8570 (mtmt) REVERT: B 213 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8646 (mp0) REVERT: C 170 LYS cc_start: 0.8718 (ttmm) cc_final: 0.8463 (ttpp) REVERT: C 179 GLN cc_start: 0.8939 (tp40) cc_final: 0.8629 (tp40) REVERT: C 183 ASN cc_start: 0.9031 (m-40) cc_final: 0.8578 (m-40) REVERT: D 113 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7924 (mt-10) REVERT: D 176 GLN cc_start: 0.5783 (pm20) cc_final: 0.5150 (pm20) REVERT: E 192 GLN cc_start: 0.9090 (tp40) cc_final: 0.8827 (tp40) REVERT: E 200 THR cc_start: 0.8928 (m) cc_final: 0.8702 (p) REVERT: F 170 LYS cc_start: 0.8787 (ttmm) cc_final: 0.8497 (ttpp) REVERT: F 195 ASN cc_start: 0.8342 (m-40) cc_final: 0.8071 (m110) REVERT: G 67 GLN cc_start: 0.8824 (tp40) cc_final: 0.8537 (tp40) REVERT: G 176 GLN cc_start: 0.5870 (pm20) cc_final: 0.5626 (pm20) REVERT: G 192 GLN cc_start: 0.9031 (tp40) cc_final: 0.8526 (tm-30) REVERT: H 154 ARG cc_start: 0.8426 (mtt90) cc_final: 0.7992 (mmt-90) REVERT: H 179 GLN cc_start: 0.8709 (tp40) cc_final: 0.8421 (tp-100) REVERT: H 197 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7861 (p0) REVERT: H 200 THR cc_start: 0.8907 (m) cc_final: 0.8622 (p) REVERT: I 170 LYS cc_start: 0.8773 (ttmm) cc_final: 0.8501 (ttpp) REVERT: I 175 GLU cc_start: 0.7731 (tp30) cc_final: 0.7348 (mt-10) REVERT: I 185 MET cc_start: 0.8121 (mtt) cc_final: 0.7791 (mtp) REVERT: J 67 GLN cc_start: 0.8755 (tp40) cc_final: 0.8472 (tp40) REVERT: J 176 GLN cc_start: 0.6512 (pm20) cc_final: 0.5960 (pm20) REVERT: J 192 GLN cc_start: 0.9142 (tp40) cc_final: 0.8795 (tm-30) REVERT: K 154 ARG cc_start: 0.8487 (mmt-90) cc_final: 0.8219 (mmt-90) REVERT: K 200 THR cc_start: 0.9046 (m) cc_final: 0.8767 (p) REVERT: L 195 ASN cc_start: 0.8410 (m-40) cc_final: 0.8007 (m110) REVERT: L 213 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8224 (mt-10) REVERT: M 67 GLN cc_start: 0.8835 (tp40) cc_final: 0.8576 (tp40) REVERT: M 68 MET cc_start: 0.8578 (mtp) cc_final: 0.8331 (mtp) REVERT: M 154 ARG cc_start: 0.8944 (mtt90) cc_final: 0.8702 (mtt90) REVERT: M 176 GLN cc_start: 0.6132 (pm20) cc_final: 0.5854 (pm20) REVERT: M 192 GLN cc_start: 0.9088 (tp40) cc_final: 0.8850 (tp40) REVERT: N 154 ARG cc_start: 0.8737 (mtt-85) cc_final: 0.8522 (mmt-90) REVERT: N 200 THR cc_start: 0.8892 (m) cc_final: 0.8633 (p) REVERT: N 213 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8571 (mt-10) REVERT: O 212 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8336 (pm20) outliers start: 23 outliers final: 17 residues processed: 472 average time/residue: 0.3269 time to fit residues: 209.4257 Evaluate side-chains 476 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 456 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain C residue 192 GLN Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain D residue 120 HIS Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain G residue 198 CYS Chi-restraints excluded: chain H residue 197 ASP Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain L residue 218 CYS Chi-restraints excluded: chain M residue 120 HIS Chi-restraints excluded: chain N residue 150 ILE Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain O residue 159 GLU Chi-restraints excluded: chain O residue 212 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 45 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 122 optimal weight: 0.0470 chunk 7 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 58 optimal weight: 0.0970 chunk 8 optimal weight: 4.9990 chunk 62 optimal weight: 0.2980 chunk 82 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 GLN G 63 GLN J 50 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.136456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.105906 restraints weight = 21579.889| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.44 r_work: 0.3217 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14155 Z= 0.118 Angle : 0.580 9.192 19205 Z= 0.295 Chirality : 0.041 0.161 2185 Planarity : 0.005 0.042 2490 Dihedral : 4.035 16.135 1890 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.47 % Allowed : 16.67 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.19), residues: 1745 helix: 1.18 (0.15), residues: 1180 sheet: -2.09 (0.48), residues: 45 loop : 1.27 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 184 HIS 0.001 0.000 HIS G 12 PHE 0.008 0.001 PHE E 168 TYR 0.014 0.001 TYR F 164 ARG 0.007 0.001 ARG G 132 Details of bonding type rmsd hydrogen bonds : bond 0.03476 ( 860) hydrogen bonds : angle 4.05770 ( 2490) covalent geometry : bond 0.00279 (14155) covalent geometry : angle 0.57955 (19205) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9612.15 seconds wall clock time: 169 minutes 20.37 seconds (10160.37 seconds total)