Starting phenix.real_space_refine on Fri May 16 14:34:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ckw_16704/05_2025/8ckw_16704.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ckw_16704/05_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_16704/05_2025/8ckw_16704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ckw_16704/05_2025/8ckw_16704.map" model { file = "/net/cci-nas-00/data/ceres_data/8ckw_16704/05_2025/8ckw_16704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ckw_16704/05_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-5687/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: 8.60, per 1000 atoms: 0.62 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: 3.31 Conformation dependent library (CDL) restraints added in 1.7 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: 1.29 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: 3.67 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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: 3.720 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: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 31.490 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.330 ------------------------------------------------------------------------------- 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 : 1.530 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: 0.3071 time to fit residues: 260.2044 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 : 1.602 ------------------------------------------------------------------------------- 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 = 0.3293 r_free = 0.3293 target = 0.103271 restraints weight = 21364.967| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.25 r_work: 0.3077 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 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 : 1.896 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: 0.8908 (m) cc_final: 0.8572 (p) REVERT: B 202 LEU cc_start: 0.8999 (mt) cc_final: 0.8756 (mt) REVERT: C 170 LYS cc_start: 0.8782 (ttmm) cc_final: 0.8530 (ttpp) REVERT: C 183 ASN cc_start: 0.9366 (m-40) cc_final: 0.9056 (m-40) REVERT: C 197 ASP cc_start: 0.8780 (p0) cc_final: 0.8535 (p0) REVERT: C 201 ILE cc_start: 0.9359 (mt) cc_final: 0.9152 (mp) REVERT: D 128 GLU cc_start: 0.8259 (tp30) cc_final: 0.8038 (tp30) REVERT: D 154 ARG cc_start: 0.8530 (mtt-85) cc_final: 0.8282 (mtt-85) REVERT: D 176 GLN cc_start: 0.6966 (pm20) cc_final: 0.6621 (pm20) REVERT: F 170 LYS cc_start: 0.8847 (ttmm) cc_final: 0.8579 (ttpp) REVERT: F 183 ASN cc_start: 0.9116 (m-40) cc_final: 0.8853 (m-40) REVERT: F 195 ASN cc_start: 0.8196 (m-40) cc_final: 0.7987 (m110) REVERT: G 67 GLN cc_start: 0.8874 (tp40) cc_final: 0.8659 (tp40) REVERT: G 176 GLN cc_start: 0.6871 (pm20) cc_final: 0.6548 (pm20) REVERT: G 192 GLN cc_start: 0.9209 (tp40) cc_final: 0.8857 (tp40) REVERT: H 192 GLN cc_start: 0.9193 (tp40) cc_final: 0.8947 (tp40) REVERT: H 195 ASN cc_start: 0.8446 (t0) cc_final: 0.8148 (t0) REVERT: I 166 ASP cc_start: 0.8628 (m-30) cc_final: 0.8285 (m-30) REVERT: I 170 LYS cc_start: 0.8876 (ttmm) cc_final: 0.8657 (ttpp) REVERT: I 175 GLU cc_start: 0.7694 (tp30) cc_final: 0.7421 (tt0) REVERT: I 183 ASN cc_start: 0.9204 (m-40) cc_final: 0.8919 (m-40) REVERT: J 162 ARG cc_start: 0.8030 (ttt90) cc_final: 0.7769 (ttp80) REVERT: J 192 GLN cc_start: 0.9126 (tp40) cc_final: 0.8783 (tp40) REVERT: K 200 THR cc_start: 0.9019 (m) cc_final: 0.8663 (p) REVERT: L 195 ASN cc_start: 0.8567 (m-40) cc_final: 0.8164 (m110) REVERT: N 200 THR cc_start: 0.8993 (m) cc_final: 0.8649 (p) REVERT: O 183 ASN cc_start: 0.9274 (m-40) cc_final: 0.8993 (m-40) outliers start: 28 outliers final: 13 residues processed: 542 average time/residue: 0.3074 time to fit residues: 225.5626 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 : 1.453 ------------------------------------------------------------------------------- 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: 0.9980 chunk 117 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 chunk 27 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3852 r_free = 0.3852 target = 0.139546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.109267 restraints weight = 21985.389| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.52 r_work: 0.3263 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14155 Z= 0.139 Angle : 0.578 10.191 19205 Z= 0.293 Chirality : 0.043 0.174 2185 Planarity : 0.005 0.040 2490 Dihedral : 4.464 19.634 1890 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.00 % Allowed : 11.80 % Favored : 86.20 % 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: 1.65 (0.19), residues: 1745 helix: 1.27 (0.14), residues: 1165 sheet: -2.50 (0.47), residues: 45 loop : 1.36 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 184 HIS 0.001 0.000 HIS D 62 PHE 0.009 0.001 PHE G 32 TYR 0.010 0.001 TYR K 169 ARG 0.008 0.001 ARG H 154 Details of bonding type rmsd hydrogen bonds : bond 0.03853 ( 860) hydrogen bonds : angle 4.15181 ( 2490) covalent geometry : bond 0.00336 (14155) covalent geometry : angle 0.57811 (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 528 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 498 time to evaluate : 1.605 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: 0.8663 (tt0) cc_final: 0.8364 (tt0) REVERT: A 66 MET cc_start: 0.9072 (tpt) cc_final: 0.8573 (tpt) REVERT: A 67 GLN cc_start: 0.8699 (tp40) cc_final: 0.8427 (tp40) REVERT: A 113 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7794 (mt-10) REVERT: A 170 LYS cc_start: 0.8496 (tptt) cc_final: 0.8290 (mmtt) REVERT: A 176 GLN cc_start: 0.6348 (pm20) cc_final: 0.6024 (pm20) REVERT: A 192 GLN cc_start: 0.9018 (tp40) cc_final: 0.8649 (tm-30) REVERT: A 198 CYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7939 (m) REVERT: C 159 GLU cc_start: 0.8515 (tt0) cc_final: 0.8238 (tt0) REVERT: C 167 ARG cc_start: 0.9132 (mtp-110) cc_final: 0.8638 (mtm110) REVERT: C 170 LYS cc_start: 0.8652 (ttmm) cc_final: 0.8386 (ttpp) REVERT: C 183 ASN cc_start: 0.9000 (m-40) cc_final: 0.8678 (m-40) REVERT: C 192 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8137 (mp-120) REVERT: D 162 ARG cc_start: 0.8235 (ttp-170) cc_final: 0.7957 (ttt-90) REVERT: E 213 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8337 (mt-10) REVERT: F 170 LYS cc_start: 0.8683 (ttmm) cc_final: 0.8397 (ttpp) REVERT: F 183 ASN cc_start: 0.8981 (m-40) cc_final: 0.8723 (m-40) REVERT: F 195 ASN cc_start: 0.8084 (m-40) cc_final: 0.7837 (m110) REVERT: F 203 LYS cc_start: 0.8492 (mttm) cc_final: 0.8279 (mmtt) REVERT: F 213 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8232 (mt-10) REVERT: H 213 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8644 (mp0) REVERT: I 170 LYS cc_start: 0.8730 (ttmm) cc_final: 0.8512 (ttpp) REVERT: I 175 GLU cc_start: 0.7722 (tp30) cc_final: 0.7424 (mt-10) REVERT: I 183 ASN cc_start: 0.9003 (m-40) cc_final: 0.8745 (m-40) REVERT: I 185 MET cc_start: 0.8037 (mtt) cc_final: 0.7778 (mtt) REVERT: J 176 GLN cc_start: 0.6477 (pm20) cc_final: 0.6145 (pm20) REVERT: J 192 GLN cc_start: 0.9027 (tp40) cc_final: 0.8710 (tp40) REVERT: K 200 THR cc_start: 0.8954 (m) cc_final: 0.8607 (p) REVERT: L 195 ASN cc_start: 0.8329 (m-40) cc_final: 0.7821 (m110) REVERT: L 213 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8072 (mt-10) REVERT: M 67 GLN cc_start: 0.8693 (tp40) cc_final: 0.8351 (tp40) REVERT: M 113 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7672 (mt-10) REVERT: M 176 GLN cc_start: 0.6846 (pm20) cc_final: 0.6465 (pm20) REVERT: M 192 GLN cc_start: 0.9076 (tp40) cc_final: 0.8735 (tp40) REVERT: M 203 LYS cc_start: 0.9070 (mmtp) cc_final: 0.8839 (mmtp) REVERT: N 200 THR cc_start: 0.8964 (m) cc_final: 0.8584 (p) REVERT: O 183 ASN cc_start: 0.9013 (m-40) cc_final: 0.8744 (m-40) REVERT: O 213 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8107 (mt-10) outliers start: 30 outliers final: 11 residues processed: 513 average time/residue: 0.3082 time to fit residues: 215.1548 Evaluate side-chains 477 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 464 time to evaluate : 1.551 ------------------------------------------------------------------------------- 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 192 GLN Chi-restraints excluded: chain F residue 218 CYS 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 58 THR Chi-restraints excluded: chain L residue 212 GLU 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: 2.9990 chunk 91 optimal weight: 0.0770 chunk 32 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 overall best weight: 0.9940 ------------------------------------------------------------------------------- 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 L 192 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.129005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.102734 restraints weight = 21405.595| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.27 r_work: 0.3095 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14155 Z= 0.144 Angle : 0.574 10.045 19205 Z= 0.290 Chirality : 0.043 0.196 2185 Planarity : 0.005 0.038 2490 Dihedral : 4.317 17.861 1890 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.80 % Allowed : 14.13 % 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: 1.68 (0.19), residues: 1745 helix: 1.31 (0.15), residues: 1165 sheet: -2.46 (0.47), residues: 45 loop : 1.35 (0.25), residues: 535 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 F 168 TYR 0.010 0.001 TYR K 169 ARG 0.008 0.001 ARG H 154 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 860) hydrogen bonds : angle 4.09214 ( 2490) covalent geometry : bond 0.00350 (14155) covalent geometry : angle 0.57420 (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 515 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 488 time to evaluate : 1.527 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: 0.9089 (tpt) cc_final: 0.8639 (tpt) REVERT: A 67 GLN cc_start: 0.8816 (tp40) cc_final: 0.8581 (tp40) REVERT: A 113 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7919 (mt-10) REVERT: A 145 TYR cc_start: 0.8970 (m-80) cc_final: 0.8664 (m-80) REVERT: A 162 ARG cc_start: 0.8400 (ttp80) cc_final: 0.8101 (ttp80) REVERT: A 170 LYS cc_start: 0.8546 (tptt) cc_final: 0.8346 (mmtt) REVERT: A 176 GLN cc_start: 0.6513 (pm20) cc_final: 0.6298 (pm20) REVERT: A 192 GLN cc_start: 0.9164 (tp40) cc_final: 0.8864 (tm-30) REVERT: A 198 CYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8083 (m) REVERT: B 200 THR cc_start: 0.8976 (m) cc_final: 0.8652 (p) REVERT: C 167 ARG cc_start: 0.9272 (mtp-110) cc_final: 0.8938 (mtp180) REVERT: C 170 LYS cc_start: 0.8781 (ttmm) cc_final: 0.8520 (ttpp) REVERT: C 179 GLN cc_start: 0.8905 (tp40) cc_final: 0.8540 (tp-100) REVERT: C 183 ASN cc_start: 0.9053 (m-40) cc_final: 0.8502 (m-40) REVERT: D 113 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7898 (mt-10) REVERT: D 170 LYS cc_start: 0.8525 (tptt) cc_final: 0.8318 (mmtm) REVERT: D 176 GLN cc_start: 0.6607 (pm20) cc_final: 0.6076 (pm20) REVERT: E 192 GLN cc_start: 0.9073 (tp40) cc_final: 0.8787 (tp40) REVERT: F 170 LYS cc_start: 0.8758 (ttmm) cc_final: 0.8479 (ttpp) REVERT: F 195 ASN cc_start: 0.8146 (m-40) cc_final: 0.7882 (m110) REVERT: F 213 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8434 (mt-10) REVERT: G 67 GLN cc_start: 0.8774 (tp40) cc_final: 0.8527 (tp40) REVERT: G 176 GLN cc_start: 0.6384 (pm20) cc_final: 0.6167 (pm20) REVERT: G 192 GLN cc_start: 0.9088 (tp40) cc_final: 0.8854 (tp40) REVERT: H 197 ASP cc_start: 0.8431 (p0) cc_final: 0.8178 (p0) REVERT: H 200 THR cc_start: 0.8961 (m) cc_final: 0.8625 (p) REVERT: I 170 LYS cc_start: 0.8839 (ttmm) cc_final: 0.8579 (ttpp) REVERT: I 175 GLU cc_start: 0.7797 (tp30) cc_final: 0.7305 (mt-10) REVERT: J 176 GLN cc_start: 0.6690 (pm20) cc_final: 0.6358 (pm20) REVERT: J 192 GLN cc_start: 0.9162 (tp40) cc_final: 0.8897 (tp40) REVERT: K 200 THR cc_start: 0.9012 (m) cc_final: 0.8716 (p) REVERT: L 195 ASN cc_start: 0.8474 (m-40) cc_final: 0.8009 (m110) REVERT: L 213 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8302 (mt-10) REVERT: M 67 GLN cc_start: 0.8832 (tp40) cc_final: 0.8616 (tp40) REVERT: M 113 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7903 (mt-10) REVERT: M 176 GLN cc_start: 0.6997 (pm20) cc_final: 0.6672 (pm20) REVERT: M 192 GLN cc_start: 0.9169 (tp40) cc_final: 0.8934 (tp40) REVERT: N 200 THR cc_start: 0.8950 (m) cc_final: 0.8620 (p) REVERT: O 183 ASN cc_start: 0.9127 (m-40) cc_final: 0.8909 (m-40) REVERT: O 203 LYS cc_start: 0.8318 (mmtp) cc_final: 0.8118 (mttm) outliers start: 27 outliers final: 16 residues processed: 501 average time/residue: 0.3120 time to fit residues: 211.9447 Evaluate side-chains 480 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 463 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR 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 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 I residue 218 CYS Chi-restraints excluded: chain J residue 2 ILE 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: 3.9990 chunk 89 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 14 optimal weight: 0.7980 chunk 110 optimal weight: 7.9990 chunk 138 optimal weight: 0.2980 chunk 85 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 O 155 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.140131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.109831 restraints weight = 22223.691| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.52 r_work: 0.3277 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3961 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= 0.134 Angle : 0.564 10.249 19205 Z= 0.284 Chirality : 0.042 0.154 2185 Planarity : 0.005 0.039 2490 Dihedral : 4.204 18.449 1890 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.53 % Allowed : 14.53 % Favored : 83.93 % 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: 1.69 (0.19), residues: 1745 helix: 1.29 (0.15), residues: 1165 sheet: -2.30 (0.50), residues: 45 loop : 1.38 (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 0.009 0.001 PHE L 168 TYR 0.010 0.001 TYR K 169 ARG 0.006 0.001 ARG H 154 Details of bonding type rmsd hydrogen bonds : bond 0.03642 ( 860) hydrogen bonds : angle 4.03288 ( 2490) covalent geometry : bond 0.00326 (14155) covalent geometry : angle 0.56373 (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 486 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 463 time to evaluate : 1.667 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: 0.9015 (tpt) cc_final: 0.8503 (tpt) REVERT: A 67 GLN cc_start: 0.8714 (tp40) cc_final: 0.8487 (tp40) REVERT: A 113 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7842 (mt-10) REVERT: A 162 ARG cc_start: 0.8247 (ttp80) cc_final: 0.7948 (ttp80) REVERT: A 198 CYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7960 (m) REVERT: B 200 THR cc_start: 0.8889 (m) cc_final: 0.8568 (p) REVERT: B 203 LYS cc_start: 0.8821 (mtpp) cc_final: 0.8479 (mtmt) REVERT: C 167 ARG cc_start: 0.9138 (mtp-110) cc_final: 0.8788 (mtp180) REVERT: C 170 LYS cc_start: 0.8627 (ttmm) cc_final: 0.8369 (ttpp) REVERT: C 179 GLN cc_start: 0.8843 (tp40) cc_final: 0.8632 (tp40) REVERT: C 183 ASN cc_start: 0.8889 (m-40) cc_final: 0.8476 (m-40) REVERT: D 68 MET cc_start: 0.8343 (mtp) cc_final: 0.7973 (mtp) REVERT: D 154 ARG cc_start: 0.8642 (mtt-85) cc_final: 0.8411 (mtt-85) REVERT: D 176 GLN cc_start: 0.6310 (pm20) cc_final: 0.6012 (pm20) REVERT: E 192 GLN cc_start: 0.9000 (tp40) cc_final: 0.8726 (tp40) REVERT: F 170 LYS cc_start: 0.8622 (ttmm) cc_final: 0.8311 (ttpp) REVERT: F 182 LYS cc_start: 0.8687 (mttm) cc_final: 0.8440 (mttp) REVERT: F 195 ASN cc_start: 0.8226 (m-40) cc_final: 0.7947 (m110) REVERT: F 213 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8253 (mt-10) REVERT: H 197 ASP cc_start: 0.8309 (p0) cc_final: 0.7998 (p0) REVERT: H 200 THR cc_start: 0.8937 (m) cc_final: 0.8624 (p) REVERT: H 213 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8396 (mp0) REVERT: I 170 LYS cc_start: 0.8732 (ttmm) cc_final: 0.8469 (ttpp) REVERT: I 175 GLU cc_start: 0.7750 (tp30) cc_final: 0.7150 (mt-10) REVERT: J 67 GLN cc_start: 0.8654 (tp40) cc_final: 0.8379 (tp40) REVERT: J 192 GLN cc_start: 0.9029 (tp40) cc_final: 0.8750 (tp40) REVERT: K 154 ARG cc_start: 0.8422 (mtt-85) cc_final: 0.8189 (mmt-90) REVERT: K 200 THR cc_start: 0.8994 (m) cc_final: 0.8694 (p) REVERT: L 179 GLN cc_start: 0.8930 (tp40) cc_final: 0.8670 (tp40) REVERT: L 195 ASN cc_start: 0.8426 (m-40) cc_final: 0.7931 (m110) REVERT: L 213 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8076 (mt-10) REVERT: M 67 GLN cc_start: 0.8696 (tp40) cc_final: 0.8394 (tp40) REVERT: M 113 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7829 (mt-10) REVERT: M 175 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6775 (mm-30) REVERT: M 176 GLN cc_start: 0.6786 (pm20) cc_final: 0.6511 (pm20) REVERT: M 192 GLN cc_start: 0.9020 (tp40) cc_final: 0.8783 (tp40) REVERT: N 200 THR cc_start: 0.8923 (m) cc_final: 0.8586 (p) REVERT: O 183 ASN cc_start: 0.8962 (m-40) cc_final: 0.8739 (m-40) REVERT: O 195 ASN cc_start: 0.8481 (m110) cc_final: 0.8170 (m-40) REVERT: O 203 LYS cc_start: 0.8334 (mmtp) cc_final: 0.8130 (mttm) outliers start: 23 outliers final: 15 residues processed: 472 average time/residue: 0.3166 time to fit residues: 201.7305 Evaluate side-chains 476 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 460 time to evaluate : 1.468 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 128 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 161 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 GLN D 50 GLN H 179 GLN M 50 GLN N 179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.131045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.100387 restraints weight = 21602.147| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.39 r_work: 0.3145 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14155 Z= 0.149 Angle : 0.577 10.102 19205 Z= 0.291 Chirality : 0.042 0.161 2185 Planarity : 0.005 0.039 2490 Dihedral : 4.204 18.084 1890 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.87 % Allowed : 14.67 % Favored : 83.47 % 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: 1.22 (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 I 184 HIS 0.002 0.000 HIS G 12 PHE 0.009 0.001 PHE G 32 TYR 0.013 0.001 TYR M 145 ARG 0.007 0.001 ARG H 154 Details of bonding type rmsd hydrogen bonds : bond 0.03732 ( 860) hydrogen bonds : angle 4.06420 ( 2490) covalent geometry : bond 0.00369 (14155) covalent geometry : angle 0.57697 (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: 28 poor density : 474 time to evaluate : 1.660 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 66 MET cc_start: 0.9098 (tpt) cc_final: 0.8645 (tpt) REVERT: A 67 GLN cc_start: 0.8823 (tp40) cc_final: 0.8551 (tp40) REVERT: A 145 TYR cc_start: 0.8791 (m-80) cc_final: 0.8497 (m-80) REVERT: A 162 ARG cc_start: 0.8399 (ttp80) cc_final: 0.8084 (ttp80) REVERT: A 176 GLN cc_start: 0.6489 (pm20) cc_final: 0.6033 (pm20) REVERT: A 192 GLN cc_start: 0.9159 (tp40) cc_final: 0.8826 (tm-30) REVERT: A 198 CYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8008 (m) REVERT: B 200 THR cc_start: 0.8973 (m) cc_final: 0.8642 (p) REVERT: B 203 LYS cc_start: 0.8877 (mtpp) cc_final: 0.8513 (mtmt) REVERT: C 170 LYS cc_start: 0.8724 (ttmm) cc_final: 0.8470 (ttpp) REVERT: C 179 GLN cc_start: 0.8905 (tp40) cc_final: 0.8665 (tp40) REVERT: C 183 ASN cc_start: 0.8962 (m-40) cc_final: 0.8511 (m-40) REVERT: C 199 LYS cc_start: 0.8919 (ttpt) cc_final: 0.8698 (ttpp) REVERT: D 154 ARG cc_start: 0.8775 (mtt-85) cc_final: 0.8537 (mtt-85) REVERT: D 176 GLN cc_start: 0.6422 (pm20) cc_final: 0.6161 (pm20) REVERT: E 192 GLN cc_start: 0.9098 (tp40) cc_final: 0.8801 (tp40) REVERT: F 170 LYS cc_start: 0.8777 (ttmm) cc_final: 0.8486 (ttpp) REVERT: F 182 LYS cc_start: 0.8785 (mttm) cc_final: 0.8560 (mttp) REVERT: F 195 ASN cc_start: 0.8250 (m-40) cc_final: 0.7954 (m110) REVERT: G 67 GLN cc_start: 0.8755 (tp40) cc_final: 0.8513 (tp40) REVERT: G 144 MET cc_start: 0.8781 (ttp) cc_final: 0.8539 (ptm) REVERT: G 176 GLN cc_start: 0.6002 (pm20) cc_final: 0.5660 (pm20) REVERT: G 192 GLN cc_start: 0.9091 (tp40) cc_final: 0.8819 (tp40) REVERT: H 197 ASP cc_start: 0.8359 (p0) cc_final: 0.8062 (p0) REVERT: H 200 THR cc_start: 0.9059 (m) cc_final: 0.8758 (p) REVERT: I 166 ASP cc_start: 0.8626 (m-30) cc_final: 0.8193 (m-30) REVERT: I 170 LYS cc_start: 0.8807 (ttmm) cc_final: 0.8551 (ttpp) REVERT: I 175 GLU cc_start: 0.7745 (tp30) cc_final: 0.7088 (mt-10) REVERT: J 67 GLN cc_start: 0.8773 (tp40) cc_final: 0.8480 (tp40) REVERT: J 176 GLN cc_start: 0.6627 (pm20) cc_final: 0.6000 (pm20) REVERT: J 192 GLN cc_start: 0.9156 (tp40) cc_final: 0.8857 (tp40) REVERT: K 154 ARG cc_start: 0.8520 (mtt-85) cc_final: 0.8274 (mmt-90) REVERT: K 200 THR cc_start: 0.9050 (m) cc_final: 0.8753 (p) REVERT: L 195 ASN cc_start: 0.8426 (m-40) cc_final: 0.7897 (m110) REVERT: L 213 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8240 (mt-10) REVERT: M 67 GLN cc_start: 0.8838 (tp40) cc_final: 0.8525 (tp40) REVERT: M 175 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6885 (mm-30) REVERT: N 200 THR cc_start: 0.9057 (m) cc_final: 0.8694 (p) REVERT: N 213 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8613 (mt-10) REVERT: O 183 ASN cc_start: 0.8983 (m-40) cc_final: 0.8570 (m110) REVERT: O 195 ASN cc_start: 0.8517 (m110) cc_final: 0.8208 (m-40) REVERT: O 203 LYS cc_start: 0.8398 (mmtp) cc_final: 0.8197 (mttm) outliers start: 28 outliers final: 22 residues processed: 485 average time/residue: 0.3371 time to fit residues: 221.0092 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 : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR 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 189 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 22 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 chunk 164 optimal weight: 0.4980 chunk 138 optimal weight: 0.5980 chunk 118 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 107 optimal weight: 0.4980 chunk 102 optimal weight: 9.9990 chunk 150 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.133579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.103264 restraints weight = 21612.813| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.39 r_work: 0.3196 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14155 Z= 0.119 Angle : 0.568 10.197 19205 Z= 0.287 Chirality : 0.041 0.167 2185 Planarity : 0.005 0.041 2490 Dihedral : 4.089 16.930 1890 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.87 % Allowed : 15.40 % Favored : 82.73 % 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: 1.62 (0.19), residues: 1745 helix: 1.24 (0.15), residues: 1170 sheet: -2.29 (0.50), residues: 45 loop : 1.36 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 184 HIS 0.001 0.000 HIS D 12 PHE 0.008 0.001 PHE L 168 TYR 0.011 0.001 TYR M 145 ARG 0.008 0.001 ARG H 154 Details of bonding type rmsd hydrogen bonds : bond 0.03493 ( 860) hydrogen bonds : angle 3.98712 ( 2490) covalent geometry : bond 0.00283 (14155) covalent geometry : angle 0.56783 (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 503 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 475 time to evaluate : 1.587 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 66 MET cc_start: 0.9064 (tpt) cc_final: 0.8702 (tpt) REVERT: A 67 GLN cc_start: 0.8804 (tp40) cc_final: 0.8548 (tp40) REVERT: A 176 GLN cc_start: 0.6307 (pm20) cc_final: 0.5689 (pm20) REVERT: A 192 GLN cc_start: 0.9146 (tp40) cc_final: 0.8829 (tm-30) REVERT: A 198 CYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7969 (m) REVERT: B 200 THR cc_start: 0.8956 (m) cc_final: 0.8647 (p) REVERT: B 203 LYS cc_start: 0.8818 (mtpp) cc_final: 0.8479 (mtmt) REVERT: B 213 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8720 (mp0) REVERT: C 170 LYS cc_start: 0.8695 (ttmm) cc_final: 0.8439 (ttpp) REVERT: C 179 GLN cc_start: 0.8940 (tp40) cc_final: 0.8671 (tp40) REVERT: C 183 ASN cc_start: 0.8910 (m-40) cc_final: 0.8502 (m-40) REVERT: D 154 ARG cc_start: 0.8734 (mtt-85) cc_final: 0.8489 (mtt-85) REVERT: D 176 GLN cc_start: 0.6366 (pm20) cc_final: 0.6129 (pm20) REVERT: E 192 GLN cc_start: 0.9079 (tp40) cc_final: 0.8839 (tp40) REVERT: E 200 THR cc_start: 0.8932 (m) cc_final: 0.8649 (p) REVERT: F 170 LYS cc_start: 0.8742 (ttmm) cc_final: 0.8450 (ttpp) REVERT: F 195 ASN cc_start: 0.8316 (m-40) cc_final: 0.8027 (m110) REVERT: G 67 GLN cc_start: 0.8826 (tp40) cc_final: 0.8559 (tp40) REVERT: G 176 GLN cc_start: 0.5582 (pm20) cc_final: 0.5190 (pm20) REVERT: G 192 GLN cc_start: 0.9047 (tp40) cc_final: 0.8799 (tp40) REVERT: H 154 ARG cc_start: 0.8534 (mtt90) cc_final: 0.8295 (mmt90) REVERT: H 179 GLN cc_start: 0.8674 (tp40) cc_final: 0.8451 (tp-100) REVERT: H 197 ASP cc_start: 0.8286 (p0) cc_final: 0.8010 (p0) REVERT: H 200 THR cc_start: 0.9036 (m) cc_final: 0.8744 (p) REVERT: I 170 LYS cc_start: 0.8799 (ttmm) cc_final: 0.8535 (ttpp) REVERT: I 175 GLU cc_start: 0.7736 (tp30) cc_final: 0.7215 (mt-10) REVERT: I 179 GLN cc_start: 0.9032 (tp40) cc_final: 0.8723 (tp40) REVERT: I 183 ASN cc_start: 0.9002 (m-40) cc_final: 0.8704 (m-40) REVERT: J 67 GLN cc_start: 0.8739 (tp40) cc_final: 0.8426 (tp40) REVERT: J 176 GLN cc_start: 0.6496 (pm20) cc_final: 0.5920 (pm20) REVERT: J 192 GLN cc_start: 0.9146 (tp40) cc_final: 0.8804 (tm-30) REVERT: K 200 THR cc_start: 0.9019 (m) cc_final: 0.8710 (p) REVERT: L 195 ASN cc_start: 0.8437 (m-40) cc_final: 0.7996 (m110) REVERT: L 213 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8216 (mt-10) REVERT: M 67 GLN cc_start: 0.8821 (tp40) cc_final: 0.8484 (tp40) REVERT: M 118 MET cc_start: 0.8066 (mtm) cc_final: 0.7832 (mtm) REVERT: M 124 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.7178 (mm) REVERT: M 176 GLN cc_start: 0.6122 (pm20) cc_final: 0.5632 (pm20) REVERT: M 192 GLN cc_start: 0.9087 (tp40) cc_final: 0.8854 (tp40) REVERT: N 154 ARG cc_start: 0.8682 (mtt-85) cc_final: 0.8425 (mmt-90) REVERT: N 200 THR cc_start: 0.8991 (m) cc_final: 0.8652 (p) REVERT: N 213 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8620 (mt-10) REVERT: O 195 ASN cc_start: 0.8502 (m110) cc_final: 0.8273 (m-40) REVERT: O 203 LYS cc_start: 0.8418 (mmtp) cc_final: 0.8201 (mttm) outliers start: 28 outliers final: 18 residues processed: 486 average time/residue: 0.3066 time to fit residues: 202.0853 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 : 1.494 ------------------------------------------------------------------------------- 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 113 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 131 optimal weight: 0.4980 chunk 6 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 138 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 50 GLN O 179 GLN O 183 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.133020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.102502 restraints weight = 21455.835| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.39 r_work: 0.3183 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14155 Z= 0.130 Angle : 0.585 10.883 19205 Z= 0.295 Chirality : 0.042 0.160 2185 Planarity : 0.005 0.041 2490 Dihedral : 4.082 16.694 1890 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.87 % Allowed : 15.60 % Favored : 82.53 % 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: 1.50 (0.19), residues: 1745 helix: 1.15 (0.15), residues: 1180 sheet: -2.30 (0.48), residues: 45 loop : 1.28 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 184 HIS 0.001 0.000 HIS D 12 PHE 0.008 0.001 PHE G 32 TYR 0.009 0.001 TYR K 169 ARG 0.009 0.001 ARG H 154 Details of bonding type rmsd hydrogen bonds : bond 0.03555 ( 860) hydrogen bonds : angle 4.01420 ( 2490) covalent geometry : bond 0.00318 (14155) covalent geometry : angle 0.58540 (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 495 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 467 time to evaluate : 1.710 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: 0.9073 (tpt) cc_final: 0.8663 (tpt) REVERT: A 67 GLN cc_start: 0.8815 (tp40) cc_final: 0.8556 (tp40) REVERT: A 176 GLN cc_start: 0.6309 (pm20) cc_final: 0.5924 (pm20) REVERT: A 192 GLN cc_start: 0.9159 (tp40) cc_final: 0.8827 (tm-30) REVERT: A 198 CYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7950 (m) REVERT: B 179 GLN cc_start: 0.8671 (tp40) cc_final: 0.8187 (tp-100) REVERT: B 183 ASN cc_start: 0.9045 (m-40) cc_final: 0.8562 (m-40) REVERT: B 200 THR cc_start: 0.8843 (m) cc_final: 0.8568 (p) REVERT: C 170 LYS cc_start: 0.8695 (ttmm) cc_final: 0.8439 (ttpp) REVERT: C 179 GLN cc_start: 0.8948 (tp40) cc_final: 0.8675 (tp40) REVERT: C 183 ASN cc_start: 0.8967 (m-40) cc_final: 0.8465 (m-40) REVERT: D 154 ARG cc_start: 0.8731 (mtt-85) cc_final: 0.8479 (mtt-85) REVERT: E 192 GLN cc_start: 0.9070 (tp40) cc_final: 0.8825 (tp40) REVERT: E 200 THR cc_start: 0.8914 (m) cc_final: 0.8664 (p) REVERT: F 170 LYS cc_start: 0.8742 (ttmm) cc_final: 0.8461 (ttpp) REVERT: F 195 ASN cc_start: 0.8334 (m-40) cc_final: 0.8088 (m110) REVERT: G 67 GLN cc_start: 0.8860 (tp40) cc_final: 0.8576 (tp40) REVERT: G 176 GLN cc_start: 0.5766 (pm20) cc_final: 0.5517 (pm20) REVERT: G 192 GLN cc_start: 0.9053 (tp40) cc_final: 0.8822 (tp40) REVERT: H 154 ARG cc_start: 0.8469 (mtt90) cc_final: 0.8066 (mmt90) REVERT: H 179 GLN cc_start: 0.8683 (tp40) cc_final: 0.8415 (tp-100) REVERT: H 197 ASP cc_start: 0.8259 (p0) cc_final: 0.7959 (p0) REVERT: H 200 THR cc_start: 0.8922 (m) cc_final: 0.8641 (p) REVERT: H 213 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8683 (mp0) REVERT: I 170 LYS cc_start: 0.8779 (ttmm) cc_final: 0.8508 (ttpp) REVERT: I 175 GLU cc_start: 0.7701 (tp30) cc_final: 0.7203 (mt-10) REVERT: I 179 GLN cc_start: 0.8999 (tp40) cc_final: 0.8657 (tp40) REVERT: I 183 ASN cc_start: 0.9004 (m-40) cc_final: 0.8708 (m-40) REVERT: J 67 GLN cc_start: 0.8738 (tp40) cc_final: 0.8415 (tp40) REVERT: J 176 GLN cc_start: 0.6488 (pm20) cc_final: 0.5954 (pm20) REVERT: J 192 GLN cc_start: 0.9159 (tp40) cc_final: 0.8811 (tm-30) REVERT: K 154 ARG cc_start: 0.8411 (mmt-90) cc_final: 0.8199 (mmt-90) REVERT: K 200 THR cc_start: 0.9026 (m) cc_final: 0.8733 (p) REVERT: L 195 ASN cc_start: 0.8408 (m-40) cc_final: 0.7974 (m110) REVERT: L 213 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8185 (mt-10) REVERT: M 67 GLN cc_start: 0.8825 (tp40) cc_final: 0.8574 (tp40) REVERT: M 68 MET cc_start: 0.8544 (mtp) cc_final: 0.8310 (mtp) REVERT: M 124 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7216 (mm) REVERT: M 154 ARG cc_start: 0.8942 (mtt90) cc_final: 0.8676 (mtt90) REVERT: M 176 GLN cc_start: 0.6060 (pm20) cc_final: 0.5775 (pm20) REVERT: M 192 GLN cc_start: 0.9101 (tp40) cc_final: 0.8865 (tp40) REVERT: N 154 ARG cc_start: 0.8669 (mtt-85) cc_final: 0.8433 (mmt-90) REVERT: N 200 THR cc_start: 0.8972 (m) cc_final: 0.8627 (p) REVERT: N 213 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8653 (mt-10) REVERT: O 195 ASN cc_start: 0.8480 (m110) cc_final: 0.8258 (m-40) REVERT: O 203 LYS cc_start: 0.8394 (mmtp) cc_final: 0.8165 (mttm) outliers start: 28 outliers final: 19 residues processed: 477 average time/residue: 0.3148 time to fit residues: 203.7708 Evaluate side-chains 477 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 456 time to evaluate : 1.583 ------------------------------------------------------------------------------- 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 189 LEU Chi-restraints excluded: chain C residue 192 GLN 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 218 CYS Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain L residue 185 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 50 optimal weight: 0.5980 chunk 10 optimal weight: 9.9990 chunk 104 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 163 optimal weight: 6.9990 chunk 3 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 50 GLN K 179 GLN M 63 GLN O 183 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.132322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.101731 restraints weight = 21493.839| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.39 r_work: 0.3166 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4269 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= 0.142 Angle : 0.608 10.996 19205 Z= 0.304 Chirality : 0.042 0.161 2185 Planarity : 0.005 0.041 2490 Dihedral : 4.113 16.599 1890 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.80 % Allowed : 16.47 % 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: 1.40 (0.19), residues: 1745 helix: 1.08 (0.15), residues: 1180 sheet: -2.30 (0.49), residues: 45 loop : 1.24 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 184 HIS 0.001 0.000 HIS D 12 PHE 0.009 0.001 PHE G 32 TYR 0.012 0.001 TYR O 169 ARG 0.007 0.001 ARG H 154 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 860) hydrogen bonds : angle 4.06028 ( 2490) covalent geometry : bond 0.00353 (14155) covalent geometry : angle 0.60813 (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 500 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 473 time to evaluate : 1.454 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: 0.9069 (tpt) cc_final: 0.8543 (tpt) REVERT: A 67 GLN cc_start: 0.8817 (tp40) cc_final: 0.8553 (tp40) REVERT: A 176 GLN cc_start: 0.6344 (pm20) cc_final: 0.5987 (pm20) REVERT: A 192 GLN cc_start: 0.9176 (tp40) cc_final: 0.8843 (tm-30) REVERT: A 198 CYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7991 (m) REVERT: B 179 GLN cc_start: 0.8686 (tp40) cc_final: 0.7964 (tp-100) REVERT: B 183 ASN cc_start: 0.9039 (m-40) cc_final: 0.8426 (m-40) REVERT: B 200 THR cc_start: 0.8828 (m) cc_final: 0.8613 (p) REVERT: B 213 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8671 (mp0) REVERT: C 170 LYS cc_start: 0.8709 (ttmm) cc_final: 0.8458 (ttpp) REVERT: C 179 GLN cc_start: 0.8960 (tp40) cc_final: 0.8682 (tp40) REVERT: C 183 ASN cc_start: 0.8839 (m-40) cc_final: 0.8435 (m-40) REVERT: D 154 ARG cc_start: 0.8752 (mtt-85) cc_final: 0.8531 (mtt-85) REVERT: D 176 GLN cc_start: 0.5978 (pm20) cc_final: 0.5263 (pm20) REVERT: E 192 GLN cc_start: 0.9080 (tp40) cc_final: 0.8815 (tp40) REVERT: E 200 THR cc_start: 0.8922 (m) cc_final: 0.8713 (p) REVERT: F 170 LYS cc_start: 0.8743 (ttmm) cc_final: 0.8463 (ttpp) REVERT: F 195 ASN cc_start: 0.8311 (m-40) cc_final: 0.8042 (m110) REVERT: G 67 GLN cc_start: 0.8860 (tp40) cc_final: 0.8581 (tp40) REVERT: G 176 GLN cc_start: 0.5747 (pm20) cc_final: 0.5489 (pm20) REVERT: G 192 GLN cc_start: 0.9066 (tp40) cc_final: 0.8831 (tp40) REVERT: H 154 ARG cc_start: 0.8495 (mtt90) cc_final: 0.8263 (mmt90) REVERT: H 179 GLN cc_start: 0.8750 (tp40) cc_final: 0.8476 (tp-100) REVERT: H 197 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7946 (p0) REVERT: H 200 THR cc_start: 0.8881 (m) cc_final: 0.8609 (p) REVERT: I 170 LYS cc_start: 0.8776 (ttmm) cc_final: 0.8503 (ttpp) REVERT: I 175 GLU cc_start: 0.7716 (tp30) cc_final: 0.7225 (mt-10) REVERT: I 179 GLN cc_start: 0.8985 (tp40) cc_final: 0.8630 (tp40) REVERT: I 183 ASN cc_start: 0.8990 (m-40) cc_final: 0.8687 (m-40) REVERT: J 67 GLN cc_start: 0.8756 (tp40) cc_final: 0.8436 (tp40) REVERT: J 176 GLN cc_start: 0.6487 (pm20) cc_final: 0.5946 (pm20) REVERT: J 192 GLN cc_start: 0.9164 (tp40) cc_final: 0.8802 (tm-30) REVERT: K 200 THR cc_start: 0.9051 (m) cc_final: 0.8764 (p) REVERT: L 195 ASN cc_start: 0.8424 (m-40) cc_final: 0.7974 (m110) REVERT: L 213 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8181 (mt-10) REVERT: M 67 GLN cc_start: 0.8839 (tp40) cc_final: 0.8585 (tp40) REVERT: M 68 MET cc_start: 0.8586 (mtp) cc_final: 0.8354 (mtp) REVERT: M 124 ILE cc_start: 0.7569 (OUTLIER) cc_final: 0.7199 (mm) REVERT: M 154 ARG cc_start: 0.8938 (mtt90) cc_final: 0.8696 (mtt90) REVERT: M 176 GLN cc_start: 0.6059 (pm20) cc_final: 0.5800 (pm20) REVERT: M 192 GLN cc_start: 0.9110 (tp40) cc_final: 0.8872 (tp40) REVERT: N 154 ARG cc_start: 0.8709 (mtt-85) cc_final: 0.8467 (mmt-90) REVERT: N 200 THR cc_start: 0.9004 (m) cc_final: 0.8670 (p) REVERT: N 213 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8682 (mt-10) REVERT: O 195 ASN cc_start: 0.8472 (m110) cc_final: 0.8249 (m-40) REVERT: O 203 LYS cc_start: 0.8407 (mmtp) cc_final: 0.8189 (mttm) REVERT: O 212 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8318 (pm20) outliers start: 27 outliers final: 16 residues processed: 482 average time/residue: 0.3072 time to fit residues: 200.3232 Evaluate side-chains 488 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 468 time to evaluate : 1.483 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 3.9990 chunk 147 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 159 optimal weight: 0.4980 chunk 125 optimal weight: 0.7980 chunk 136 optimal weight: 0.6980 chunk 140 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 GLN F 219 GLN I 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.133556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.103076 restraints weight = 21505.480| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.39 r_work: 0.3187 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14155 Z= 0.128 Angle : 0.601 10.711 19205 Z= 0.303 Chirality : 0.042 0.163 2185 Planarity : 0.005 0.041 2490 Dihedral : 4.079 16.074 1890 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.53 % Allowed : 16.93 % Favored : 81.53 % 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: 1.37 (0.19), residues: 1745 helix: 1.06 (0.15), residues: 1180 sheet: -2.28 (0.50), residues: 45 loop : 1.24 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 23 HIS 0.001 0.000 HIS D 12 PHE 0.008 0.001 PHE E 168 TYR 0.010 0.001 TYR K 169 ARG 0.007 0.001 ARG H 154 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 860) hydrogen bonds : angle 4.07223 ( 2490) covalent geometry : bond 0.00314 (14155) covalent geometry : angle 0.60145 (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 501 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 478 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: A 66 MET cc_start: 0.9068 (tpt) cc_final: 0.8691 (tpt) REVERT: A 67 GLN cc_start: 0.8807 (tp40) cc_final: 0.8548 (tp40) REVERT: A 145 TYR cc_start: 0.8752 (m-80) cc_final: 0.8446 (m-80) REVERT: A 192 GLN cc_start: 0.9154 (tp40) cc_final: 0.8821 (tm-30) REVERT: A 198 CYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7966 (m) REVERT: B 179 GLN cc_start: 0.8608 (tp40) cc_final: 0.8011 (tp-100) REVERT: B 183 ASN cc_start: 0.9050 (m-40) cc_final: 0.8500 (m-40) REVERT: B 200 THR cc_start: 0.8814 (m) cc_final: 0.8607 (p) REVERT: B 213 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8658 (mp0) REVERT: C 170 LYS cc_start: 0.8699 (ttmm) cc_final: 0.8442 (ttpp) REVERT: C 179 GLN cc_start: 0.8978 (tp40) cc_final: 0.8696 (tp40) REVERT: C 183 ASN cc_start: 0.8861 (m-40) cc_final: 0.8480 (m-40) REVERT: D 53 ASN cc_start: 0.8735 (m-40) cc_final: 0.8498 (m-40) REVERT: D 154 ARG cc_start: 0.8743 (mtt-85) cc_final: 0.8525 (mtt-85) REVERT: D 176 GLN cc_start: 0.5877 (pm20) cc_final: 0.5154 (pm20) REVERT: E 192 GLN cc_start: 0.9080 (tp40) cc_final: 0.8815 (tp40) REVERT: E 200 THR cc_start: 0.8913 (m) cc_final: 0.8711 (p) REVERT: F 170 LYS cc_start: 0.8732 (ttmm) cc_final: 0.8427 (ttpp) REVERT: F 195 ASN cc_start: 0.8307 (m-40) cc_final: 0.8028 (m110) REVERT: G 67 GLN cc_start: 0.8838 (tp40) cc_final: 0.8557 (tp40) REVERT: G 176 GLN cc_start: 0.5587 (pm20) cc_final: 0.5323 (pm20) REVERT: G 192 GLN cc_start: 0.9046 (tp40) cc_final: 0.8813 (tp40) REVERT: H 154 ARG cc_start: 0.8461 (mtt90) cc_final: 0.8232 (mmt90) REVERT: H 179 GLN cc_start: 0.8754 (tp40) cc_final: 0.8473 (tp-100) REVERT: H 197 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.7980 (p0) REVERT: H 200 THR cc_start: 0.8859 (m) cc_final: 0.8606 (p) REVERT: H 213 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8723 (mp0) REVERT: I 170 LYS cc_start: 0.8769 (ttmm) cc_final: 0.8506 (ttpp) REVERT: I 175 GLU cc_start: 0.7700 (tp30) cc_final: 0.7226 (mt-10) REVERT: I 179 GLN cc_start: 0.8976 (tp40) cc_final: 0.8614 (tp40) REVERT: I 183 ASN cc_start: 0.9017 (m-40) cc_final: 0.8722 (m-40) REVERT: J 176 GLN cc_start: 0.6419 (pm20) cc_final: 0.5897 (pm20) REVERT: J 192 GLN cc_start: 0.9159 (tp40) cc_final: 0.8807 (tm-30) REVERT: K 200 THR cc_start: 0.9045 (m) cc_final: 0.8770 (p) REVERT: L 195 ASN cc_start: 0.8427 (m-40) cc_final: 0.8024 (m110) REVERT: L 213 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8186 (mt-10) REVERT: M 67 GLN cc_start: 0.8827 (tp40) cc_final: 0.8576 (tp40) REVERT: M 68 MET cc_start: 0.8571 (mtp) cc_final: 0.8339 (mtp) REVERT: M 118 MET cc_start: 0.8040 (mtm) cc_final: 0.7823 (mtm) REVERT: M 124 ILE cc_start: 0.7468 (OUTLIER) cc_final: 0.7092 (mm) REVERT: M 154 ARG cc_start: 0.8934 (mtt90) cc_final: 0.8682 (mtt90) REVERT: M 176 GLN cc_start: 0.5924 (pm20) cc_final: 0.5665 (pm20) REVERT: M 192 GLN cc_start: 0.9097 (tp40) cc_final: 0.8862 (tp40) REVERT: N 154 ARG cc_start: 0.8698 (mtt-85) cc_final: 0.8474 (mmt-90) REVERT: N 200 THR cc_start: 0.8993 (m) cc_final: 0.8664 (p) REVERT: N 213 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8676 (mt-10) REVERT: O 203 LYS cc_start: 0.8388 (mmtp) cc_final: 0.8167 (mttm) REVERT: O 212 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8302 (pm20) outliers start: 23 outliers final: 17 residues processed: 486 average time/residue: 0.3120 time to fit residues: 205.3510 Evaluate side-chains 488 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 467 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 45 optimal weight: 0.7980 chunk 90 optimal weight: 0.2980 chunk 93 optimal weight: 5.9990 chunk 122 optimal weight: 0.0010 chunk 7 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 62 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN D 50 GLN G 63 GLN L 179 GLN L 183 ASN O 155 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.133622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.107082 restraints weight = 21622.727| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.36 r_work: 0.3169 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14155 Z= 0.121 Angle : 0.592 10.329 19205 Z= 0.300 Chirality : 0.041 0.163 2185 Planarity : 0.005 0.041 2490 Dihedral : 4.031 15.521 1890 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.60 % Allowed : 17.07 % Favored : 81.33 % 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: 1.45 (0.19), residues: 1745 helix: 1.12 (0.15), residues: 1180 sheet: -2.18 (0.52), residues: 45 loop : 1.25 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 184 HIS 0.001 0.000 HIS G 12 PHE 0.008 0.001 PHE E 168 TYR 0.011 0.001 TYR O 169 ARG 0.007 0.001 ARG H 154 Details of bonding type rmsd hydrogen bonds : bond 0.03543 ( 860) hydrogen bonds : angle 4.04685 ( 2490) covalent geometry : bond 0.00291 (14155) covalent geometry : angle 0.59161 (19205) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9320.23 seconds wall clock time: 161 minutes 27.42 seconds (9687.42 seconds total)