Starting phenix.real_space_refine on Thu Sep 18 06:03:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ckw_16704/09_2025/8ckw_16704.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ckw_16704/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ckw_16704/09_2025/8ckw_16704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ckw_16704/09_2025/8ckw_16704.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ckw_16704/09_2025/8ckw_16704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ckw_16704/09_2025/8ckw_16704.map" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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, 'ASN:plan1': 1, 'GLU:plan': 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, 'ASN:plan1': 1, 'GLU:plan': 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, 'ASN:plan1': 1, 'GLU:plan': 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, 'ASN:plan1': 1, 'GLU:plan': 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, 'ASN:plan1': 1, 'GLU:plan': 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: 3.45, per 1000 atoms: 0.25 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: 1.15 Conformation dependent library (CDL) restraints added in 489.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.42 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: 2.04 Time building geometry restraints manager: 1.46 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: 0.02 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: 3.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.860 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.410 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.017 0.002 ARG F 167 TYR 0.026 0.005 TYR G 169 PHE 0.021 0.003 PHE G 40 TRP 0.017 0.005 TRP J 184 HIS 0.009 0.004 HIS J 12 Details of bonding type rmsd covalent geometry : bond 0.00484 (14155) covalent geometry : angle 0.86960 (19205) hydrogen bonds : bond 0.12795 ( 860) hydrogen bonds : angle 6.00068 ( 2490) *********************** 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 : 0.706 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: 0.1506 time to fit residues: 128.3230 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 : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 = 0.3622 r_free = 0.3622 target = 0.129120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.104047 restraints weight = 21424.767| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.19 r_work: 0.3081 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14155 Z= 0.156 Angle : 0.624 10.997 19205 Z= 0.315 Chirality : 0.043 0.150 2185 Planarity : 0.005 0.036 2490 Dihedral : 4.739 19.961 1890 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.80 % Allowed : 10.47 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.18), residues: 1745 helix: 0.98 (0.14), residues: 1150 sheet: -2.35 (0.49), residues: 45 loop : 1.22 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 154 TYR 0.010 0.001 TYR K 169 PHE 0.008 0.001 PHE J 40 TRP 0.012 0.001 TRP F 184 HIS 0.002 0.001 HIS J 120 Details of bonding type rmsd covalent geometry : bond 0.00384 (14155) covalent geometry : angle 0.62401 (19205) hydrogen bonds : bond 0.04303 ( 860) hydrogen bonds : angle 4.32928 ( 2490) *********************** 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 553 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 526 time to evaluate : 0.569 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: 0.9142 (tpt) cc_final: 0.8744 (tpt) REVERT: B 200 THR cc_start: 0.8898 (m) cc_final: 0.8566 (p) REVERT: B 202 LEU cc_start: 0.9018 (mt) cc_final: 0.8779 (mt) REVERT: C 170 LYS cc_start: 0.8791 (ttmm) cc_final: 0.8542 (ttpp) REVERT: C 183 ASN cc_start: 0.9373 (m-40) cc_final: 0.9066 (m-40) REVERT: C 197 ASP cc_start: 0.8755 (p0) cc_final: 0.8517 (p0) REVERT: D 128 GLU cc_start: 0.8257 (tp30) cc_final: 0.8047 (tp30) REVERT: D 176 GLN cc_start: 0.6983 (pm20) cc_final: 0.6642 (pm20) REVERT: F 170 LYS cc_start: 0.8862 (ttmm) cc_final: 0.8600 (ttpp) REVERT: F 183 ASN cc_start: 0.9116 (m-40) cc_final: 0.8857 (m-40) REVERT: F 195 ASN cc_start: 0.8181 (m-40) cc_final: 0.7973 (m110) REVERT: G 67 GLN cc_start: 0.8876 (tp40) cc_final: 0.8665 (tp40) REVERT: G 176 GLN cc_start: 0.6874 (pm20) cc_final: 0.6544 (pm20) REVERT: G 192 GLN cc_start: 0.9200 (tp40) cc_final: 0.8847 (tp40) REVERT: H 192 GLN cc_start: 0.9184 (tp40) cc_final: 0.8937 (tp40) REVERT: H 195 ASN cc_start: 0.8399 (t0) cc_final: 0.8142 (t0) REVERT: I 166 ASP cc_start: 0.8623 (m-30) cc_final: 0.8263 (m-30) REVERT: I 170 LYS cc_start: 0.8878 (ttmm) cc_final: 0.8663 (ttpp) REVERT: I 175 GLU cc_start: 0.7696 (tp30) cc_final: 0.7467 (tt0) REVERT: I 183 ASN cc_start: 0.9212 (m-40) cc_final: 0.8931 (m-40) REVERT: J 162 ARG cc_start: 0.8005 (ttt90) cc_final: 0.7745 (ttp80) REVERT: J 192 GLN cc_start: 0.9118 (tp40) cc_final: 0.8776 (tp40) REVERT: K 200 THR cc_start: 0.9006 (m) cc_final: 0.8654 (p) REVERT: L 195 ASN cc_start: 0.8573 (m-40) cc_final: 0.8183 (m110) REVERT: N 200 THR cc_start: 0.8985 (m) cc_final: 0.8648 (p) REVERT: O 183 ASN cc_start: 0.9282 (m-40) cc_final: 0.9001 (m-40) outliers start: 27 outliers final: 13 residues processed: 543 average time/residue: 0.1458 time to fit residues: 108.0903 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 : 0.561 ------------------------------------------------------------------------------- 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 40 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 I 195 ASN O 195 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.136294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.105483 restraints weight = 22050.340| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.53 r_work: 0.3207 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14155 Z= 0.195 Angle : 0.626 11.492 19205 Z= 0.314 Chirality : 0.045 0.185 2185 Planarity : 0.005 0.038 2490 Dihedral : 4.599 18.722 1890 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.20 % Allowed : 11.73 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.19), residues: 1745 helix: 1.12 (0.14), residues: 1150 sheet: -2.65 (0.43), residues: 45 loop : 1.25 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 154 TYR 0.012 0.002 TYR K 169 PHE 0.012 0.002 PHE M 32 TRP 0.010 0.001 TRP C 184 HIS 0.002 0.001 HIS G 12 Details of bonding type rmsd covalent geometry : bond 0.00485 (14155) covalent geometry : angle 0.62643 (19205) hydrogen bonds : bond 0.04166 ( 860) hydrogen bonds : angle 4.29658 ( 2490) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 489 time to evaluate : 0.580 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 50 GLN cc_start: 0.8736 (tt0) cc_final: 0.8443 (tt0) REVERT: A 66 MET cc_start: 0.9074 (tpt) cc_final: 0.8635 (tpt) REVERT: A 67 GLN cc_start: 0.8718 (tp40) cc_final: 0.8441 (tp40) REVERT: A 111 LEU cc_start: 0.8153 (tt) cc_final: 0.7944 (tp) REVERT: A 176 GLN cc_start: 0.6499 (pm20) cc_final: 0.6184 (pm20) REVERT: A 192 GLN cc_start: 0.9031 (tp40) cc_final: 0.8667 (tm-30) REVERT: A 198 CYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7994 (m) REVERT: C 159 GLU cc_start: 0.8564 (tt0) cc_final: 0.8279 (tt0) REVERT: C 167 ARG cc_start: 0.9123 (mtp-110) cc_final: 0.8632 (mtm110) REVERT: C 170 LYS cc_start: 0.8686 (ttmm) cc_final: 0.8420 (ttpp) REVERT: C 179 GLN cc_start: 0.8872 (tp40) cc_final: 0.8627 (tp-100) REVERT: C 183 ASN cc_start: 0.9057 (m-40) cc_final: 0.8529 (m-40) REVERT: C 192 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8192 (mp-120) REVERT: D 33 SER cc_start: 0.8888 (t) cc_final: 0.8570 (m) REVERT: F 170 LYS cc_start: 0.8684 (ttmm) cc_final: 0.8388 (ttpp) REVERT: F 183 ASN cc_start: 0.9025 (m-40) cc_final: 0.8754 (m-40) REVERT: F 195 ASN cc_start: 0.8147 (m-40) cc_final: 0.7935 (m110) REVERT: G 113 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7780 (mt-10) REVERT: G 198 CYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7990 (m) REVERT: H 213 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8685 (mp0) REVERT: I 166 ASP cc_start: 0.8484 (m-30) cc_final: 0.8113 (m-30) REVERT: I 170 LYS cc_start: 0.8768 (ttmm) cc_final: 0.8534 (ttpp) REVERT: I 175 GLU cc_start: 0.7719 (tp30) cc_final: 0.7294 (tt0) REVERT: I 183 ASN cc_start: 0.9038 (m-40) cc_final: 0.8754 (m-40) REVERT: I 185 MET cc_start: 0.8140 (mtt) cc_final: 0.7901 (mtt) REVERT: I 195 ASN cc_start: 0.8201 (m-40) cc_final: 0.7998 (m110) REVERT: J 67 GLN cc_start: 0.8646 (tp40) cc_final: 0.8364 (tp40) REVERT: J 176 GLN cc_start: 0.6626 (pm20) cc_final: 0.6255 (pm20) REVERT: J 192 GLN cc_start: 0.9039 (tp40) cc_final: 0.8704 (tp40) REVERT: K 200 THR cc_start: 0.8976 (m) cc_final: 0.8627 (p) REVERT: L 213 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8087 (mt-10) REVERT: M 67 GLN cc_start: 0.8755 (tp40) cc_final: 0.8467 (tp40) REVERT: M 113 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7607 (mt-10) REVERT: M 176 GLN cc_start: 0.6962 (pm20) cc_final: 0.6548 (pm20) REVERT: M 192 GLN cc_start: 0.9098 (tp40) cc_final: 0.8746 (tp40) REVERT: M 199 LYS cc_start: 0.8868 (ttpt) cc_final: 0.8665 (ttpt) REVERT: M 203 LYS cc_start: 0.9089 (mmtp) cc_final: 0.8850 (mmtp) REVERT: N 200 THR cc_start: 0.8975 (m) cc_final: 0.8592 (p) REVERT: O 183 ASN cc_start: 0.9040 (m-40) cc_final: 0.8763 (m-40) REVERT: O 213 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8119 (mt-10) outliers start: 33 outliers final: 16 residues processed: 505 average time/residue: 0.1464 time to fit residues: 100.7540 Evaluate side-chains 490 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 471 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR 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 218 CYS Chi-restraints excluded: chain G residue 20 LEU 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 58 THR Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 198 CYS 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 205 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 89 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 1 optimal weight: 0.2980 chunk 64 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 193 ASN J 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.139903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.109600 restraints weight = 22122.163| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.52 r_work: 0.3273 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3782 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= 0.133 Angle : 0.566 9.092 19205 Z= 0.286 Chirality : 0.042 0.191 2185 Planarity : 0.005 0.039 2490 Dihedral : 4.326 18.432 1890 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.07 % Allowed : 14.07 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.19), residues: 1745 helix: 1.22 (0.15), residues: 1175 sheet: -2.44 (0.47), residues: 45 loop : 1.19 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 154 TYR 0.010 0.001 TYR K 169 PHE 0.010 0.001 PHE F 168 TRP 0.009 0.001 TRP C 184 HIS 0.001 0.000 HIS J 12 Details of bonding type rmsd covalent geometry : bond 0.00321 (14155) covalent geometry : angle 0.56612 (19205) hydrogen bonds : bond 0.03747 ( 860) hydrogen bonds : angle 4.10007 ( 2490) *********************** 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 525 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 494 time to evaluate : 0.534 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 50 GLN cc_start: 0.8611 (tt0) cc_final: 0.8329 (tt0) REVERT: A 66 MET cc_start: 0.9011 (tpt) cc_final: 0.8532 (tpt) REVERT: A 67 GLN cc_start: 0.8720 (tp40) cc_final: 0.8485 (tp40) REVERT: A 113 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7810 (mt-10) REVERT: A 145 TYR cc_start: 0.8775 (m-80) cc_final: 0.8465 (m-80) REVERT: A 162 ARG cc_start: 0.8304 (ttp80) cc_final: 0.8093 (ttp80) REVERT: A 192 GLN cc_start: 0.9015 (tp40) cc_final: 0.8673 (tm-30) REVERT: A 198 CYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7971 (m) REVERT: B 200 THR cc_start: 0.8881 (m) cc_final: 0.8573 (p) REVERT: C 167 ARG cc_start: 0.9161 (mtp-110) cc_final: 0.8753 (mtp180) REVERT: C 170 LYS cc_start: 0.8655 (ttmm) cc_final: 0.8404 (ttpp) REVERT: C 179 GLN cc_start: 0.8797 (tp40) cc_final: 0.8422 (tp-100) REVERT: C 183 ASN cc_start: 0.8904 (m-40) cc_final: 0.8265 (m110) REVERT: D 113 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7808 (mt-10) REVERT: D 176 GLN cc_start: 0.6404 (pm20) cc_final: 0.5898 (pm20) REVERT: E 192 GLN cc_start: 0.8988 (tp40) cc_final: 0.8694 (tp40) REVERT: F 170 LYS cc_start: 0.8661 (ttmm) cc_final: 0.8352 (ttpp) REVERT: F 195 ASN cc_start: 0.8132 (m-40) cc_final: 0.7834 (m110) REVERT: G 67 GLN cc_start: 0.8767 (tp40) cc_final: 0.8469 (tp40) REVERT: G 113 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7796 (mt-10) REVERT: G 176 GLN cc_start: 0.6272 (pm20) cc_final: 0.5973 (pm20) REVERT: G 192 GLN cc_start: 0.9017 (tp40) cc_final: 0.8511 (tm-30) REVERT: I 170 LYS cc_start: 0.8740 (ttmm) cc_final: 0.8512 (ttpp) REVERT: I 175 GLU cc_start: 0.7787 (tp30) cc_final: 0.7278 (mt-10) REVERT: J 162 ARG cc_start: 0.7927 (ttt90) cc_final: 0.7663 (ttp80) REVERT: J 192 GLN cc_start: 0.9025 (tp40) cc_final: 0.8731 (tp40) REVERT: J 198 CYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7943 (m) REVERT: K 200 THR cc_start: 0.8957 (m) cc_final: 0.8658 (p) REVERT: L 192 GLN cc_start: 0.8907 (mm110) cc_final: 0.8699 (mm110) REVERT: L 195 ASN cc_start: 0.8402 (m-40) cc_final: 0.7903 (m110) REVERT: L 213 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8109 (mt-10) REVERT: M 13 GLN cc_start: 0.8219 (tm-30) cc_final: 0.7846 (tt0) REVERT: M 67 GLN cc_start: 0.8697 (tp40) cc_final: 0.8380 (tp40) REVERT: M 113 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7768 (mt-10) REVERT: M 176 GLN cc_start: 0.6879 (pm20) cc_final: 0.6469 (pm20) REVERT: M 192 GLN cc_start: 0.9082 (tp40) cc_final: 0.8781 (tp40) REVERT: N 200 THR cc_start: 0.8939 (m) cc_final: 0.8602 (p) REVERT: O 183 ASN cc_start: 0.8971 (m-40) cc_final: 0.8742 (m-40) outliers start: 31 outliers final: 11 residues processed: 509 average time/residue: 0.1545 time to fit residues: 106.7338 Evaluate side-chains 475 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 462 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 F residue 192 GLN Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain I residue 218 CYS 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 M residue 58 THR Chi-restraints excluded: chain M residue 120 HIS Chi-restraints excluded: chain M residue 124 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 57 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 77 optimal weight: 0.0570 chunk 132 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- 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 J 50 GLN M 50 GLN O 195 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.139415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.108914 restraints weight = 22218.229| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.53 r_work: 0.3263 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14155 Z= 0.141 Angle : 0.568 10.332 19205 Z= 0.288 Chirality : 0.042 0.157 2185 Planarity : 0.005 0.039 2490 Dihedral : 4.236 18.490 1890 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.93 % Allowed : 14.80 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.19), residues: 1745 helix: 1.23 (0.15), residues: 1175 sheet: -2.34 (0.50), residues: 45 loop : 1.19 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 154 TYR 0.011 0.001 TYR K 169 PHE 0.009 0.001 PHE G 32 TRP 0.009 0.001 TRP O 184 HIS 0.001 0.000 HIS G 12 Details of bonding type rmsd covalent geometry : bond 0.00344 (14155) covalent geometry : angle 0.56751 (19205) hydrogen bonds : bond 0.03685 ( 860) hydrogen bonds : angle 4.05504 ( 2490) *********************** 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 497 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 468 time to evaluate : 0.576 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: 0.9041 (tpt) cc_final: 0.8566 (tpt) REVERT: A 67 GLN cc_start: 0.8699 (tp40) cc_final: 0.8454 (tp40) REVERT: A 113 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7778 (mt-10) REVERT: A 176 GLN cc_start: 0.6154 (pm20) cc_final: 0.5842 (pm20) REVERT: A 192 GLN cc_start: 0.9034 (tp40) cc_final: 0.8702 (tm-30) REVERT: A 198 CYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7978 (m) REVERT: B 200 THR cc_start: 0.8817 (m) cc_final: 0.8564 (p) REVERT: C 170 LYS cc_start: 0.8670 (ttmm) cc_final: 0.8411 (ttpp) REVERT: C 183 ASN cc_start: 0.8927 (m-40) cc_final: 0.8504 (m-40) REVERT: D 176 GLN cc_start: 0.6312 (pm20) cc_final: 0.6036 (pm20) REVERT: E 192 GLN cc_start: 0.8987 (tp40) cc_final: 0.8712 (tp40) REVERT: E 213 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8508 (mt-10) REVERT: F 170 LYS cc_start: 0.8668 (ttmm) cc_final: 0.8364 (ttpp) REVERT: F 182 LYS cc_start: 0.8665 (mttm) cc_final: 0.8433 (mttp) REVERT: F 195 ASN cc_start: 0.8243 (m-40) cc_final: 0.7937 (m110) REVERT: H 154 ARG cc_start: 0.8395 (mtt90) cc_final: 0.8067 (mmt-90) REVERT: H 200 THR cc_start: 0.8906 (m) cc_final: 0.8574 (p) REVERT: I 170 LYS cc_start: 0.8746 (ttmm) cc_final: 0.8524 (ttpp) REVERT: I 175 GLU cc_start: 0.7899 (tp30) cc_final: 0.7398 (tt0) REVERT: J 67 GLN cc_start: 0.8641 (tp40) cc_final: 0.8368 (tp40) REVERT: J 162 ARG cc_start: 0.7896 (ttt90) cc_final: 0.7652 (ttp80) REVERT: J 192 GLN cc_start: 0.9033 (tp40) cc_final: 0.8753 (tp40) REVERT: J 198 CYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7951 (m) REVERT: K 200 THR cc_start: 0.8984 (m) cc_final: 0.8664 (p) REVERT: L 192 GLN cc_start: 0.8891 (mm110) cc_final: 0.8679 (mm110) REVERT: L 195 ASN cc_start: 0.8401 (m-40) cc_final: 0.7910 (m110) REVERT: L 213 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8101 (mt-10) REVERT: M 67 GLN cc_start: 0.8708 (tp40) cc_final: 0.8401 (tp40) REVERT: M 113 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7824 (mt-10) REVERT: M 176 GLN cc_start: 0.6921 (pm20) cc_final: 0.6599 (pm20) REVERT: N 200 THR cc_start: 0.8961 (m) cc_final: 0.8629 (p) REVERT: O 183 ASN cc_start: 0.8953 (m-40) cc_final: 0.8706 (m-40) REVERT: O 195 ASN cc_start: 0.8429 (m-40) cc_final: 0.8203 (m110) outliers start: 29 outliers final: 16 residues processed: 481 average time/residue: 0.1517 time to fit residues: 98.9134 Evaluate side-chains 468 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 450 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain D residue 45 GLU 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 I residue 189 LEU Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 198 CYS 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 44 optimal weight: 0.3980 chunk 27 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 141 optimal weight: 0.4980 chunk 74 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 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 H 179 GLN J 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.140774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.109941 restraints weight = 22070.361| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.59 r_work: 0.3275 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14155 Z= 0.118 Angle : 0.550 8.381 19205 Z= 0.280 Chirality : 0.041 0.155 2185 Planarity : 0.005 0.040 2490 Dihedral : 4.097 17.145 1890 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.53 % Allowed : 15.67 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.19), residues: 1745 helix: 1.25 (0.15), residues: 1180 sheet: -2.32 (0.49), residues: 45 loop : 1.27 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 132 TYR 0.012 0.001 TYR O 169 PHE 0.007 0.001 PHE B 168 TRP 0.008 0.001 TRP A 184 HIS 0.001 0.000 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00280 (14155) covalent geometry : angle 0.55008 (19205) hydrogen bonds : bond 0.03516 ( 860) hydrogen bonds : angle 4.00245 ( 2490) *********************** 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 492 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 469 time to evaluate : 0.565 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 50 GLN cc_start: 0.8496 (tt0) cc_final: 0.8167 (tt0) REVERT: A 66 MET cc_start: 0.9030 (tpt) cc_final: 0.8528 (tpt) REVERT: A 67 GLN cc_start: 0.8692 (tp40) cc_final: 0.8480 (tp40) REVERT: A 113 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7890 (mt-10) REVERT: A 176 GLN cc_start: 0.5990 (pm20) cc_final: 0.5495 (pm20) REVERT: A 192 GLN cc_start: 0.9045 (tp40) cc_final: 0.8723 (tm-30) REVERT: A 198 CYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7945 (m) REVERT: B 200 THR cc_start: 0.8762 (m) cc_final: 0.8518 (p) REVERT: C 170 LYS cc_start: 0.8636 (ttmm) cc_final: 0.8363 (ttpp) REVERT: C 179 GLN cc_start: 0.8940 (tp40) cc_final: 0.8651 (tp40) REVERT: C 183 ASN cc_start: 0.8935 (m-40) cc_final: 0.8555 (m-40) REVERT: C 199 LYS cc_start: 0.8887 (ttpt) cc_final: 0.8639 (ttpp) REVERT: C 203 LYS cc_start: 0.8541 (mttm) cc_final: 0.8318 (mmtt) REVERT: E 192 GLN cc_start: 0.8981 (tp40) cc_final: 0.8728 (tp40) REVERT: F 170 LYS cc_start: 0.8643 (ttmm) cc_final: 0.8340 (ttpp) REVERT: F 179 GLN cc_start: 0.8815 (tp40) cc_final: 0.8578 (tp40) REVERT: F 195 ASN cc_start: 0.8289 (m-40) cc_final: 0.8014 (m110) REVERT: G 68 MET cc_start: 0.8487 (mtp) cc_final: 0.8236 (mtp) REVERT: H 154 ARG cc_start: 0.8384 (mtt90) cc_final: 0.8045 (mmt-90) REVERT: H 200 THR cc_start: 0.8924 (m) cc_final: 0.8608 (p) REVERT: I 170 LYS cc_start: 0.8717 (ttmm) cc_final: 0.8448 (ttpp) REVERT: I 175 GLU cc_start: 0.7707 (tp30) cc_final: 0.7254 (mt-10) REVERT: J 67 GLN cc_start: 0.8641 (tp40) cc_final: 0.8342 (tp40) REVERT: J 162 ARG cc_start: 0.7878 (ttt90) cc_final: 0.7629 (ttp80) REVERT: J 192 GLN cc_start: 0.9039 (tp40) cc_final: 0.8702 (tm-30) REVERT: J 198 CYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7883 (m) REVERT: K 200 THR cc_start: 0.8958 (m) cc_final: 0.8686 (p) REVERT: L 192 GLN cc_start: 0.8888 (mm110) cc_final: 0.8675 (mm110) REVERT: L 195 ASN cc_start: 0.8395 (m-40) cc_final: 0.7904 (m110) REVERT: L 213 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8059 (mt-10) REVERT: M 67 GLN cc_start: 0.8697 (tp40) cc_final: 0.8371 (tp40) REVERT: M 176 GLN cc_start: 0.6943 (pm20) cc_final: 0.6721 (pm20) REVERT: N 200 THR cc_start: 0.8887 (m) cc_final: 0.8571 (p) REVERT: O 183 ASN cc_start: 0.8806 (m-40) cc_final: 0.8256 (m-40) outliers start: 23 outliers final: 16 residues processed: 477 average time/residue: 0.1532 time to fit residues: 99.0815 Evaluate side-chains 476 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 458 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 J residue 2 ILE Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 198 CYS 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 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 20 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 141 optimal weight: 0.9980 chunk 109 optimal weight: 0.0470 chunk 33 optimal weight: 0.0980 chunk 105 optimal weight: 0.6980 chunk 53 optimal weight: 0.4980 chunk 152 optimal weight: 0.0470 chunk 46 optimal weight: 1.9990 overall best weight: 0.2776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 GLN C 155 GLN D 50 GLN N 193 ASN O 155 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.136388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.106676 restraints weight = 21483.402| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.39 r_work: 0.3247 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14155 Z= 0.109 Angle : 0.550 8.575 19205 Z= 0.283 Chirality : 0.040 0.163 2185 Planarity : 0.005 0.041 2490 Dihedral : 4.006 17.941 1890 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.53 % Allowed : 16.20 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.19), residues: 1745 helix: 1.32 (0.15), residues: 1180 sheet: -2.25 (0.51), residues: 45 loop : 1.28 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 132 TYR 0.007 0.001 TYR F 169 PHE 0.009 0.001 PHE E 168 TRP 0.009 0.001 TRP C 184 HIS 0.001 0.000 HIS G 62 Details of bonding type rmsd covalent geometry : bond 0.00247 (14155) covalent geometry : angle 0.55031 (19205) hydrogen bonds : bond 0.03332 ( 860) hydrogen bonds : angle 3.91707 ( 2490) *********************** 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 495 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 472 time to evaluate : 0.583 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: 0.9033 (tpt) cc_final: 0.8675 (tpt) REVERT: A 67 GLN cc_start: 0.8758 (tp40) cc_final: 0.8522 (tp40) REVERT: A 176 GLN cc_start: 0.5946 (pm20) cc_final: 0.5452 (pm20) REVERT: A 192 GLN cc_start: 0.9147 (tp40) cc_final: 0.8836 (tm-30) REVERT: A 198 CYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7920 (m) REVERT: B 183 ASN cc_start: 0.9028 (m-40) cc_final: 0.8525 (m-40) REVERT: B 200 THR cc_start: 0.8782 (m) cc_final: 0.8559 (p) REVERT: B 213 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8715 (mp0) REVERT: C 169 TYR cc_start: 0.8730 (m-80) cc_final: 0.8524 (m-80) REVERT: C 170 LYS cc_start: 0.8690 (ttmm) cc_final: 0.8417 (ttpp) REVERT: C 179 GLN cc_start: 0.8971 (tp40) cc_final: 0.8620 (tp40) REVERT: C 183 ASN cc_start: 0.8926 (m-40) cc_final: 0.8598 (m-40) REVERT: C 203 LYS cc_start: 0.8522 (mttm) cc_final: 0.8267 (mmtt) REVERT: D 176 GLN cc_start: 0.5903 (pm20) cc_final: 0.5207 (pm20) REVERT: E 192 GLN cc_start: 0.9091 (tp40) cc_final: 0.8856 (tp40) REVERT: F 170 LYS cc_start: 0.8703 (ttmm) cc_final: 0.8418 (ttpp) REVERT: F 179 GLN cc_start: 0.8823 (tp40) cc_final: 0.8554 (tp40) REVERT: F 195 ASN cc_start: 0.8346 (m-40) cc_final: 0.8067 (m110) REVERT: G 67 GLN cc_start: 0.8823 (tp40) cc_final: 0.8565 (tp40) REVERT: G 176 GLN cc_start: 0.5440 (pm20) cc_final: 0.4937 (pm20) REVERT: G 192 GLN cc_start: 0.9053 (tp40) cc_final: 0.8816 (tm-30) REVERT: H 154 ARG cc_start: 0.8347 (mtt90) cc_final: 0.7998 (mmt-90) REVERT: H 179 GLN cc_start: 0.8717 (tp40) cc_final: 0.8493 (tp-100) REVERT: I 170 LYS cc_start: 0.8797 (ttmm) cc_final: 0.8530 (ttpp) REVERT: I 175 GLU cc_start: 0.7752 (tp30) cc_final: 0.7329 (mt-10) REVERT: I 179 GLN cc_start: 0.8907 (tp40) cc_final: 0.8681 (tp40) REVERT: J 67 GLN cc_start: 0.8710 (tp40) cc_final: 0.8397 (tp40) REVERT: J 162 ARG cc_start: 0.7881 (ttt90) cc_final: 0.7676 (ttp80) REVERT: J 198 CYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7838 (m) REVERT: J 203 LYS cc_start: 0.9130 (mmtp) cc_final: 0.8915 (mttp) REVERT: K 154 ARG cc_start: 0.8317 (mtt-85) cc_final: 0.8031 (mmt-90) REVERT: K 200 THR cc_start: 0.8979 (m) cc_final: 0.8673 (p) REVERT: L 171 THR cc_start: 0.8662 (m) cc_final: 0.8453 (p) REVERT: L 195 ASN cc_start: 0.8418 (m-40) cc_final: 0.7983 (m110) REVERT: M 68 MET cc_start: 0.8520 (mtp) cc_final: 0.8289 (mtp) REVERT: M 113 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8064 (mt-10) REVERT: M 124 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.7322 (mm) REVERT: M 154 ARG cc_start: 0.8968 (mtt90) cc_final: 0.8712 (mtt90) REVERT: N 154 ARG cc_start: 0.8578 (mtt-85) cc_final: 0.8207 (mmt-90) REVERT: N 200 THR cc_start: 0.8921 (m) cc_final: 0.8610 (p) REVERT: N 213 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8708 (mt-10) REVERT: O 213 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8468 (mm-30) outliers start: 23 outliers final: 11 residues processed: 484 average time/residue: 0.1542 time to fit residues: 101.5467 Evaluate side-chains 461 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 447 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 F residue 192 GLN Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain J residue 198 CYS 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 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 150 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 68 optimal weight: 10.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN C 155 GLN D 50 GLN K 179 GLN M 63 GLN O 179 GLN O 183 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.139811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.108483 restraints weight = 21932.048| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.59 r_work: 0.3252 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14155 Z= 0.152 Angle : 0.588 9.515 19205 Z= 0.301 Chirality : 0.043 0.161 2185 Planarity : 0.005 0.040 2490 Dihedral : 4.132 17.955 1890 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.73 % Allowed : 16.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.19), residues: 1745 helix: 1.15 (0.15), residues: 1180 sheet: -2.32 (0.49), residues: 45 loop : 1.22 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 132 TYR 0.020 0.001 TYR O 164 PHE 0.009 0.001 PHE M 32 TRP 0.008 0.001 TRP A 184 HIS 0.002 0.000 HIS G 12 Details of bonding type rmsd covalent geometry : bond 0.00376 (14155) covalent geometry : angle 0.58824 (19205) hydrogen bonds : bond 0.03680 ( 860) hydrogen bonds : angle 4.08554 ( 2490) *********************** 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 493 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 467 time to evaluate : 0.446 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: 0.9027 (tpt) cc_final: 0.8635 (tpt) REVERT: A 67 GLN cc_start: 0.8673 (tp40) cc_final: 0.8430 (tp40) REVERT: A 111 LEU cc_start: 0.8186 (tp) cc_final: 0.7977 (tt) REVERT: A 176 GLN cc_start: 0.6011 (pm20) cc_final: 0.5772 (pm20) REVERT: A 192 GLN cc_start: 0.9043 (tp40) cc_final: 0.8601 (tm-30) REVERT: A 198 CYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8004 (m) REVERT: B 179 GLN cc_start: 0.8627 (tp40) cc_final: 0.8162 (tp-100) REVERT: B 183 ASN cc_start: 0.8970 (m-40) cc_final: 0.8482 (m-40) REVERT: C 170 LYS cc_start: 0.8617 (ttmm) cc_final: 0.8334 (ttpp) REVERT: C 179 GLN cc_start: 0.8951 (tp40) cc_final: 0.8587 (tp40) REVERT: C 183 ASN cc_start: 0.8892 (m-40) cc_final: 0.8526 (m-40) REVERT: D 176 GLN cc_start: 0.5916 (pm20) cc_final: 0.5240 (pm20) REVERT: E 192 GLN cc_start: 0.9001 (tp40) cc_final: 0.8752 (tp40) REVERT: E 200 THR cc_start: 0.8865 (m) cc_final: 0.8574 (p) REVERT: F 170 LYS cc_start: 0.8645 (ttmm) cc_final: 0.8338 (ttpp) REVERT: F 179 GLN cc_start: 0.8815 (tp40) cc_final: 0.8595 (tp40) REVERT: F 195 ASN cc_start: 0.8353 (m-40) cc_final: 0.8095 (m110) REVERT: G 67 GLN cc_start: 0.8741 (tp40) cc_final: 0.8464 (tp40) REVERT: G 176 GLN cc_start: 0.5675 (pm20) cc_final: 0.5412 (pm20) REVERT: G 192 GLN cc_start: 0.8983 (tp40) cc_final: 0.8760 (tp40) REVERT: H 154 ARG cc_start: 0.8416 (mtt90) cc_final: 0.8144 (mmt-90) REVERT: H 179 GLN cc_start: 0.8776 (tp40) cc_final: 0.8501 (tp-100) REVERT: I 166 ASP cc_start: 0.8417 (m-30) cc_final: 0.7980 (m-30) REVERT: I 170 LYS cc_start: 0.8744 (ttmm) cc_final: 0.8473 (ttpp) REVERT: I 175 GLU cc_start: 0.7720 (tp30) cc_final: 0.7301 (mt-10) REVERT: J 67 GLN cc_start: 0.8643 (tp40) cc_final: 0.8314 (tp40) REVERT: J 162 ARG cc_start: 0.7814 (ttt90) cc_final: 0.7610 (ttp80) REVERT: J 198 CYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7804 (m) REVERT: J 203 LYS cc_start: 0.9064 (mmtp) cc_final: 0.8822 (mttp) REVERT: K 200 THR cc_start: 0.8944 (m) cc_final: 0.8673 (p) REVERT: L 195 ASN cc_start: 0.8411 (m-40) cc_final: 0.7960 (m110) REVERT: M 13 GLN cc_start: 0.7964 (tm-30) cc_final: 0.7654 (tt0) REVERT: M 67 GLN cc_start: 0.8697 (tp40) cc_final: 0.8381 (tp40) REVERT: M 124 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7220 (mm) REVERT: M 154 ARG cc_start: 0.8856 (mtt90) cc_final: 0.8599 (mtt90) REVERT: M 176 GLN cc_start: 0.6626 (pm20) cc_final: 0.6143 (pm20) REVERT: M 192 GLN cc_start: 0.8984 (tp40) cc_final: 0.8746 (tp40) REVERT: N 154 ARG cc_start: 0.8565 (mtt-85) cc_final: 0.8263 (mmt-90) REVERT: N 200 THR cc_start: 0.8903 (m) cc_final: 0.8609 (p) REVERT: N 213 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8645 (mt-10) REVERT: O 213 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8414 (mm-30) outliers start: 26 outliers final: 18 residues processed: 478 average time/residue: 0.1580 time to fit residues: 102.8957 Evaluate side-chains 476 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 455 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain C residue 155 GLN 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 I residue 218 CYS Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 198 CYS 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 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 137 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 47 optimal weight: 0.0870 chunk 2 optimal weight: 0.5980 chunk 143 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 114 optimal weight: 0.5980 chunk 70 optimal weight: 0.2980 chunk 163 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 M 50 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.134562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.104163 restraints weight = 21526.184| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.41 r_work: 0.3200 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14155 Z= 0.118 Angle : 0.564 9.262 19205 Z= 0.291 Chirality : 0.041 0.156 2185 Planarity : 0.005 0.041 2490 Dihedral : 4.058 16.214 1890 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.20 % Allowed : 17.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.19), residues: 1745 helix: 1.19 (0.15), residues: 1180 sheet: -2.17 (0.52), residues: 45 loop : 1.28 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 154 TYR 0.014 0.001 TYR L 164 PHE 0.008 0.001 PHE E 168 TRP 0.008 0.001 TRP A 184 HIS 0.001 0.000 HIS D 12 Details of bonding type rmsd covalent geometry : bond 0.00279 (14155) covalent geometry : angle 0.56385 (19205) hydrogen bonds : bond 0.03498 ( 860) hydrogen bonds : angle 4.03268 ( 2490) *********************** 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 490 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 472 time to evaluate : 0.593 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: 0.9041 (tpt) cc_final: 0.8641 (tpt) REVERT: A 67 GLN cc_start: 0.8801 (tp40) cc_final: 0.8557 (tp40) REVERT: A 113 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8040 (mt-10) REVERT: A 176 GLN cc_start: 0.6032 (pm20) cc_final: 0.5809 (pm20) REVERT: A 192 GLN cc_start: 0.9156 (tp40) cc_final: 0.8832 (tm-30) REVERT: A 198 CYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7932 (m) REVERT: B 179 GLN cc_start: 0.8595 (tp40) cc_final: 0.8125 (tp-100) REVERT: B 183 ASN cc_start: 0.9038 (m-40) cc_final: 0.8545 (m-40) REVERT: B 213 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8666 (mp0) REVERT: C 170 LYS cc_start: 0.8702 (ttmm) cc_final: 0.8436 (ttpp) REVERT: C 179 GLN cc_start: 0.8997 (tp40) cc_final: 0.8619 (tp40) REVERT: C 183 ASN cc_start: 0.8886 (m-40) cc_final: 0.8608 (m-40) REVERT: D 176 GLN cc_start: 0.5893 (pm20) cc_final: 0.5476 (pm20) REVERT: D 203 LYS cc_start: 0.9127 (mmtp) cc_final: 0.8836 (mmtt) REVERT: E 192 GLN cc_start: 0.9097 (tp40) cc_final: 0.8851 (tp40) REVERT: E 200 THR cc_start: 0.8924 (m) cc_final: 0.8654 (p) REVERT: F 170 LYS cc_start: 0.8713 (ttmm) cc_final: 0.8416 (ttpp) REVERT: F 195 ASN cc_start: 0.8307 (m-40) cc_final: 0.8040 (m110) REVERT: G 67 GLN cc_start: 0.8884 (tp40) cc_final: 0.8597 (tp40) REVERT: G 176 GLN cc_start: 0.5723 (pm20) cc_final: 0.5455 (pm20) REVERT: G 192 GLN cc_start: 0.9057 (tp40) cc_final: 0.8533 (tm-30) REVERT: H 154 ARG cc_start: 0.8477 (mtt90) cc_final: 0.8182 (mmt-90) REVERT: H 179 GLN cc_start: 0.8780 (tp40) cc_final: 0.8498 (tp-100) REVERT: I 170 LYS cc_start: 0.8802 (ttmm) cc_final: 0.8537 (ttpp) REVERT: I 175 GLU cc_start: 0.7763 (tp30) cc_final: 0.7340 (mt-10) REVERT: J 67 GLN cc_start: 0.8737 (tp40) cc_final: 0.8406 (tp40) REVERT: J 198 CYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7845 (m) REVERT: J 203 LYS cc_start: 0.9112 (mmtp) cc_final: 0.8891 (mttp) REVERT: K 183 ASN cc_start: 0.9000 (m-40) cc_final: 0.8781 (m-40) REVERT: K 200 THR cc_start: 0.9028 (m) cc_final: 0.8745 (p) REVERT: L 195 ASN cc_start: 0.8406 (m-40) cc_final: 0.7974 (m110) REVERT: M 67 GLN cc_start: 0.8831 (tp40) cc_final: 0.8581 (tp40) REVERT: M 118 MET cc_start: 0.8093 (mtm) cc_final: 0.7866 (mtm) REVERT: M 176 GLN cc_start: 0.6663 (pm20) cc_final: 0.6156 (pm20) REVERT: M 192 GLN cc_start: 0.9089 (tp40) cc_final: 0.8789 (tm-30) REVERT: N 154 ARG cc_start: 0.8608 (mtt-85) cc_final: 0.8331 (mmt-90) REVERT: N 200 THR cc_start: 0.8980 (m) cc_final: 0.8663 (p) REVERT: N 213 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8735 (mt-10) REVERT: O 212 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8184 (pm20) REVERT: O 213 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8494 (mm-30) outliers start: 18 outliers final: 14 residues processed: 478 average time/residue: 0.1568 time to fit residues: 102.2971 Evaluate side-chains 477 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 460 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 I residue 218 CYS Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain L residue 218 CYS Chi-restraints excluded: chain M residue 120 HIS Chi-restraints excluded: chain N residue 150 ILE Chi-restraints excluded: chain 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 94 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 chunk 160 optimal weight: 0.4980 chunk 122 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 GLN D 219 GLN I 179 GLN I 183 ASN I 195 ASN L 179 GLN L 183 ASN M 50 GLN ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 219 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.136105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.104507 restraints weight = 22138.231| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.57 r_work: 0.3184 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 14155 Z= 0.232 Angle : 0.668 9.941 19205 Z= 0.339 Chirality : 0.046 0.171 2185 Planarity : 0.005 0.042 2490 Dihedral : 4.461 20.922 1890 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.20 % Allowed : 18.00 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.18), residues: 1745 helix: 0.83 (0.15), residues: 1165 sheet: -2.39 (0.48), residues: 45 loop : 1.12 (0.23), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 132 TYR 0.016 0.002 TYR O 164 PHE 0.012 0.002 PHE M 32 TRP 0.008 0.002 TRP D 133 HIS 0.003 0.001 HIS A 62 Details of bonding type rmsd covalent geometry : bond 0.00580 (14155) covalent geometry : angle 0.66821 (19205) hydrogen bonds : bond 0.04227 ( 860) hydrogen bonds : angle 4.30434 ( 2490) ********************** 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 489 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 471 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8509 (tt0) cc_final: 0.8264 (tt0) REVERT: A 66 MET cc_start: 0.9054 (tpt) cc_final: 0.8641 (tpt) REVERT: A 67 GLN cc_start: 0.8752 (tp40) cc_final: 0.8493 (tp40) REVERT: A 192 GLN cc_start: 0.9051 (tp40) cc_final: 0.8686 (tm-30) REVERT: A 198 CYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8025 (m) REVERT: C 170 LYS cc_start: 0.8654 (ttmm) cc_final: 0.8381 (ttpp) REVERT: C 179 GLN cc_start: 0.8989 (tp40) cc_final: 0.8546 (tp40) REVERT: C 183 ASN cc_start: 0.8888 (m-40) cc_final: 0.8464 (m110) REVERT: C 213 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8151 (mt-10) REVERT: D 154 ARG cc_start: 0.8791 (mtt90) cc_final: 0.8473 (mtt-85) REVERT: D 176 GLN cc_start: 0.6020 (pm20) cc_final: 0.5609 (pm20) REVERT: E 192 GLN cc_start: 0.9036 (tp40) cc_final: 0.8781 (tp40) REVERT: E 200 THR cc_start: 0.8953 (m) cc_final: 0.8671 (p) REVERT: E 213 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8554 (mt-10) REVERT: F 170 LYS cc_start: 0.8682 (ttmm) cc_final: 0.8399 (ttpp) REVERT: G 33 SER cc_start: 0.9048 (t) cc_final: 0.8678 (m) REVERT: G 67 GLN cc_start: 0.8796 (tp40) cc_final: 0.8568 (tp40) REVERT: G 176 GLN cc_start: 0.5923 (pm20) cc_final: 0.5665 (pm20) REVERT: G 192 GLN cc_start: 0.9035 (tp40) cc_final: 0.8543 (tm-30) REVERT: H 154 ARG cc_start: 0.8502 (mtt90) cc_final: 0.8186 (mmt-90) REVERT: I 170 LYS cc_start: 0.8743 (ttmm) cc_final: 0.8467 (ttpp) REVERT: I 175 GLU cc_start: 0.7796 (tp30) cc_final: 0.7184 (tt0) REVERT: J 33 SER cc_start: 0.9029 (t) cc_final: 0.8662 (m) REVERT: J 67 GLN cc_start: 0.8697 (tp40) cc_final: 0.8375 (tp40) REVERT: J 162 ARG cc_start: 0.7926 (ttt90) cc_final: 0.7590 (ttp80) REVERT: K 200 THR cc_start: 0.8987 (m) cc_final: 0.8716 (p) REVERT: L 195 ASN cc_start: 0.8377 (m-40) cc_final: 0.7873 (m110) REVERT: M 33 SER cc_start: 0.9040 (t) cc_final: 0.8604 (m) REVERT: M 67 GLN cc_start: 0.8774 (tp40) cc_final: 0.8535 (tp40) REVERT: M 176 GLN cc_start: 0.6535 (pm20) cc_final: 0.6073 (pm20) REVERT: M 192 GLN cc_start: 0.9023 (tp40) cc_final: 0.8765 (tp40) REVERT: N 179 GLN cc_start: 0.8869 (tp40) cc_final: 0.8642 (tp-100) REVERT: N 200 THR cc_start: 0.8996 (m) cc_final: 0.8690 (p) REVERT: N 213 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8659 (mt-10) REVERT: O 212 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8297 (pm20) REVERT: O 213 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8378 (mt-10) outliers start: 18 outliers final: 15 residues processed: 477 average time/residue: 0.1611 time to fit residues: 103.8270 Evaluate side-chains 474 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 457 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain C residue 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 I residue 218 CYS Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain J residue 198 CYS Chi-restraints excluded: chain L residue 218 CYS Chi-restraints excluded: chain M residue 120 HIS 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 41 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 84 optimal weight: 0.4980 chunk 142 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** G 63 GLN I 183 ASN ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 219 GLN ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.140356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.109326 restraints weight = 22119.863| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.58 r_work: 0.3263 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14155 Z= 0.130 Angle : 0.595 10.371 19205 Z= 0.306 Chirality : 0.042 0.162 2185 Planarity : 0.005 0.040 2490 Dihedral : 4.199 17.573 1890 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.07 % Allowed : 18.33 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.19), residues: 1745 helix: 0.97 (0.15), residues: 1180 sheet: -2.30 (0.51), residues: 45 loop : 1.15 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 154 TYR 0.016 0.001 TYR F 164 PHE 0.008 0.001 PHE E 168 TRP 0.009 0.001 TRP I 184 HIS 0.001 0.000 HIS D 12 Details of bonding type rmsd covalent geometry : bond 0.00313 (14155) covalent geometry : angle 0.59461 (19205) hydrogen bonds : bond 0.03713 ( 860) hydrogen bonds : angle 4.19624 ( 2490) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4340.87 seconds wall clock time: 75 minutes 4.68 seconds (4504.68 seconds total)