Starting phenix.real_space_refine on Fri Sep 27 00:53:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckw_16704/09_2024/8ckw_16704.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckw_16704/09_2024/8ckw_16704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckw_16704/09_2024/8ckw_16704.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckw_16704/09_2024/8ckw_16704.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckw_16704/09_2024/8ckw_16704.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ckw_16704/09_2024/8ckw_16704.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1045 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 8745 2.51 5 N 2390 2.21 5 O 2650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13890 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1612 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "C" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "D" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1612 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "F" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "G" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1612 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "I" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "J" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1612 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "K" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "L" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "M" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1612 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "N" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "O" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 583 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Time building chain proxies: 9.47, per 1000 atoms: 0.68 Number of scatterers: 13890 At special positions: 0 Unit cell: (148.8, 153.45, 95.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 2650 8.00 N 2390 7.00 C 8745 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.73 Conformation dependent library (CDL) restraints added in 2.6 seconds 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3360 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 5 sheets defined 74.8% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 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: 4.65 Time building geometry restraints manager: 4.37 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: 0.00 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: 4.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 35.350 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.110 ------------------------------------------------------------------------------- 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= 0.307 Angle : 0.870 13.695 19205 Z= 0.503 Chirality : 0.075 1.231 2185 Planarity : 0.008 0.083 2490 Dihedral : 12.554 78.172 5340 Min Nonbonded Distance : 0.523 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.17), residues: 1745 helix: -0.72 (0.12), residues: 1165 sheet: -2.36 (0.48), residues: 45 loop : 0.86 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.005 TRP J 184 HIS 0.009 0.004 HIS J 12 PHE 0.021 0.003 PHE G 40 TYR 0.026 0.005 TYR G 169 ARG 0.017 0.002 ARG F 167 *********************** 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 fitting. rotamer outliers: 0 poor density : 627 time to evaluate : 1.621 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: 0.3111 time to fit residues: 263.5600 Evaluate side-chains 516 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 516 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 0.2980 chunk 99 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS C 192 GLN F 192 GLN F 219 GLN H 155 GLN H 193 ASN M 219 GLN O 195 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14155 Z= 0.248 Angle : 0.624 10.789 19205 Z= 0.315 Chirality : 0.043 0.153 2185 Planarity : 0.005 0.036 2490 Dihedral : 4.744 19.846 1890 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 1.87 % Allowed : 10.47 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.18), residues: 1745 helix: 0.98 (0.14), residues: 1150 sheet: -2.34 (0.48), residues: 45 loop : 1.21 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 184 HIS 0.002 0.001 HIS G 12 PHE 0.009 0.001 PHE J 40 TYR 0.011 0.001 TYR K 169 ARG 0.007 0.001 ARG N 154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 524 time to evaluate : 1.693 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: 0.8895 (tpt) cc_final: 0.8465 (tpt) REVERT: B 179 GLN cc_start: 0.8512 (tp40) cc_final: 0.8279 (tp-100) REVERT: B 200 THR cc_start: 0.8592 (m) cc_final: 0.8351 (p) REVERT: B 202 LEU cc_start: 0.8975 (mt) cc_final: 0.8765 (mt) REVERT: C 170 LYS cc_start: 0.8533 (ttmm) cc_final: 0.8268 (ttpp) REVERT: C 183 ASN cc_start: 0.9199 (m-40) cc_final: 0.8867 (m-40) REVERT: D 128 GLU cc_start: 0.7731 (tp30) cc_final: 0.7474 (tp30) REVERT: D 154 ARG cc_start: 0.8175 (mtt-85) cc_final: 0.7913 (mtt-85) REVERT: D 176 GLN cc_start: 0.6540 (pm20) cc_final: 0.6210 (pm20) REVERT: F 170 LYS cc_start: 0.8575 (ttmm) cc_final: 0.8267 (ttpp) REVERT: F 183 ASN cc_start: 0.8999 (m-40) cc_final: 0.8723 (m-40) REVERT: F 195 ASN cc_start: 0.8139 (m-40) cc_final: 0.7920 (m110) REVERT: G 176 GLN cc_start: 0.6418 (pm20) cc_final: 0.6130 (pm20) REVERT: G 192 GLN cc_start: 0.8798 (tp40) cc_final: 0.8476 (tp40) REVERT: H 192 GLN cc_start: 0.8933 (tp40) cc_final: 0.8689 (tp40) REVERT: H 195 ASN cc_start: 0.8135 (t0) cc_final: 0.7734 (t0) REVERT: I 166 ASP cc_start: 0.8221 (m-30) cc_final: 0.7799 (m-30) REVERT: I 170 LYS cc_start: 0.8588 (ttmm) cc_final: 0.8347 (ttpp) REVERT: I 183 ASN cc_start: 0.9061 (m-40) cc_final: 0.8771 (m-40) REVERT: J 162 ARG cc_start: 0.7850 (ttt90) cc_final: 0.7625 (ttp80) REVERT: J 192 GLN cc_start: 0.8716 (tp40) cc_final: 0.8402 (tp40) REVERT: K 200 THR cc_start: 0.8689 (m) cc_final: 0.8422 (p) REVERT: L 170 LYS cc_start: 0.8436 (tttm) cc_final: 0.8216 (ttpp) REVERT: L 195 ASN cc_start: 0.8484 (m-40) cc_final: 0.8080 (m110) REVERT: N 200 THR cc_start: 0.8713 (m) cc_final: 0.8425 (p) REVERT: O 183 ASN cc_start: 0.9134 (m-40) cc_final: 0.8852 (m-40) outliers start: 28 outliers final: 13 residues processed: 542 average time/residue: 0.3082 time to fit residues: 226.9997 Evaluate side-chains 499 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 486 time to evaluate : 1.668 ------------------------------------------------------------------------------- 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 85 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 128 optimal weight: 0.0980 chunk 105 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 154 optimal weight: 0.9990 chunk 167 optimal weight: 5.9990 chunk 137 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 ASN H 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14155 Z= 0.223 Angle : 0.585 10.361 19205 Z= 0.296 Chirality : 0.043 0.173 2185 Planarity : 0.005 0.040 2490 Dihedral : 4.470 19.421 1890 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.93 % Allowed : 12.07 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.19), residues: 1745 helix: 1.26 (0.14), residues: 1165 sheet: -2.53 (0.46), residues: 45 loop : 1.35 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 184 HIS 0.001 0.001 HIS J 12 PHE 0.009 0.001 PHE G 32 TYR 0.010 0.001 TYR K 169 ARG 0.008 0.001 ARG H 154 *********************** 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 fitting. rotamer outliers: 29 poor density : 493 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLN cc_start: 0.8272 (tt0) cc_final: 0.7984 (tt0) REVERT: A 66 MET cc_start: 0.8882 (tpt) cc_final: 0.8368 (tpt) REVERT: A 170 LYS cc_start: 0.8306 (tptt) cc_final: 0.8104 (mmtt) REVERT: A 176 GLN cc_start: 0.6229 (pm20) cc_final: 0.5941 (pm20) REVERT: A 192 GLN cc_start: 0.8722 (tp40) cc_final: 0.8431 (tm-30) REVERT: C 167 ARG cc_start: 0.9071 (mtp-110) cc_final: 0.8570 (mtm110) REVERT: C 170 LYS cc_start: 0.8560 (ttmm) cc_final: 0.8302 (ttpp) REVERT: C 183 ASN cc_start: 0.8928 (m-40) cc_final: 0.8628 (m-40) REVERT: C 192 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8048 (mp-120) REVERT: D 162 ARG cc_start: 0.8121 (ttp-170) cc_final: 0.7887 (ttt-90) REVERT: F 170 LYS cc_start: 0.8569 (ttmm) cc_final: 0.8272 (ttpp) REVERT: F 183 ASN cc_start: 0.8924 (m-40) cc_final: 0.8682 (m-40) REVERT: F 195 ASN cc_start: 0.8077 (m-40) cc_final: 0.7839 (m110) REVERT: F 213 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7992 (mt-10) REVERT: I 170 LYS cc_start: 0.8592 (ttmm) cc_final: 0.8369 (ttpp) REVERT: I 183 ASN cc_start: 0.8970 (m-40) cc_final: 0.8728 (m-40) REVERT: J 176 GLN cc_start: 0.6365 (pm20) cc_final: 0.6066 (pm20) REVERT: J 192 GLN cc_start: 0.8723 (tp40) cc_final: 0.8491 (tp40) REVERT: K 200 THR cc_start: 0.8733 (m) cc_final: 0.8513 (p) REVERT: L 195 ASN cc_start: 0.8313 (m-40) cc_final: 0.7829 (m110) REVERT: L 213 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7842 (mt-10) REVERT: M 67 GLN cc_start: 0.8196 (tp40) cc_final: 0.7966 (tp40) REVERT: M 176 GLN cc_start: 0.6724 (pm20) cc_final: 0.6411 (pm20) REVERT: M 192 GLN cc_start: 0.8747 (tp40) cc_final: 0.8496 (tp40) REVERT: N 200 THR cc_start: 0.8741 (m) cc_final: 0.8480 (p) REVERT: O 183 ASN cc_start: 0.8981 (m-40) cc_final: 0.8728 (m-40) REVERT: O 213 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7839 (mt-10) outliers start: 29 outliers final: 9 residues processed: 508 average time/residue: 0.3096 time to fit residues: 212.6462 Evaluate side-chains 472 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 462 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 192 GLN Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain G residue 198 CYS Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain O residue 212 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 73 optimal weight: 0.4980 chunk 103 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 GLN C 195 ASN D 50 GLN H 179 GLN J 50 GLN L 192 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 14155 Z= 0.399 Angle : 0.654 12.121 19205 Z= 0.327 Chirality : 0.046 0.170 2185 Planarity : 0.005 0.041 2490 Dihedral : 4.565 19.226 1890 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.40 % Allowed : 13.27 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.19), residues: 1745 helix: 1.04 (0.14), residues: 1165 sheet: -2.73 (0.42), residues: 45 loop : 1.20 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 184 HIS 0.002 0.001 HIS G 62 PHE 0.013 0.002 PHE M 32 TYR 0.013 0.002 TYR K 169 ARG 0.008 0.001 ARG H 154 *********************** 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 499 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 463 time to evaluate : 1.652 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: 0.8825 (tpt) cc_final: 0.8406 (tpt) REVERT: C 159 GLU cc_start: 0.8474 (tt0) cc_final: 0.8151 (tt0) REVERT: C 167 ARG cc_start: 0.9049 (mtp-110) cc_final: 0.8527 (mtm110) REVERT: C 170 LYS cc_start: 0.8578 (ttmm) cc_final: 0.8326 (ttpp) REVERT: C 179 GLN cc_start: 0.8715 (tp40) cc_final: 0.8353 (tp-100) REVERT: C 183 ASN cc_start: 0.8905 (m-40) cc_final: 0.8233 (m-40) REVERT: D 33 SER cc_start: 0.8872 (t) cc_final: 0.8524 (m) REVERT: D 154 ARG cc_start: 0.8279 (mtt-85) cc_final: 0.8023 (mtt-85) REVERT: D 176 GLN cc_start: 0.6420 (pm20) cc_final: 0.5910 (pm20) REVERT: E 192 GLN cc_start: 0.8763 (tp40) cc_final: 0.8519 (tp40) REVERT: F 170 LYS cc_start: 0.8591 (ttmm) cc_final: 0.8268 (ttpp) REVERT: F 183 ASN cc_start: 0.8881 (m-40) cc_final: 0.8666 (m-40) REVERT: F 195 ASN cc_start: 0.8154 (m-40) cc_final: 0.7906 (m110) REVERT: I 166 ASP cc_start: 0.8228 (m-30) cc_final: 0.7814 (m-30) REVERT: I 170 LYS cc_start: 0.8633 (ttmm) cc_final: 0.8366 (ttpp) REVERT: J 33 SER cc_start: 0.8881 (t) cc_final: 0.8551 (m) REVERT: J 67 GLN cc_start: 0.8197 (tp40) cc_final: 0.7988 (tp40) REVERT: J 192 GLN cc_start: 0.8742 (tp40) cc_final: 0.8491 (tp40) REVERT: K 200 THR cc_start: 0.8811 (m) cc_final: 0.8561 (p) REVERT: L 213 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7896 (mt-10) REVERT: M 33 SER cc_start: 0.8859 (t) cc_final: 0.8445 (m) REVERT: M 176 GLN cc_start: 0.6828 (pm20) cc_final: 0.6551 (pm20) REVERT: N 200 THR cc_start: 0.8774 (m) cc_final: 0.8494 (p) REVERT: O 183 ASN cc_start: 0.8983 (m-40) cc_final: 0.8755 (m-40) outliers start: 36 outliers final: 22 residues processed: 477 average time/residue: 0.3151 time to fit residues: 202.9779 Evaluate side-chains 474 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 452 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 189 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 G residue 20 LEU Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain G residue 198 CYS Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 120 HIS Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain M residue 197 ASP Chi-restraints excluded: chain N residue 210 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 2 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 H 193 ASN J 50 GLN M 50 GLN O 195 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14155 Z= 0.216 Angle : 0.581 10.304 19205 Z= 0.292 Chirality : 0.042 0.158 2185 Planarity : 0.005 0.040 2490 Dihedral : 4.313 18.877 1890 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.53 % Allowed : 14.93 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.19), residues: 1745 helix: 1.16 (0.14), residues: 1165 sheet: -2.47 (0.50), residues: 45 loop : 1.27 (0.24), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 184 HIS 0.001 0.000 HIS A 12 PHE 0.008 0.001 PHE G 32 TYR 0.011 0.001 TYR F 164 ARG 0.008 0.001 ARG H 154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 465 time to evaluate : 1.828 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: 0.8816 (tpt) cc_final: 0.8347 (tpt) REVERT: A 145 TYR cc_start: 0.8459 (m-80) cc_final: 0.8128 (m-80) REVERT: A 176 GLN cc_start: 0.6081 (pm20) cc_final: 0.5800 (pm20) REVERT: A 192 GLN cc_start: 0.8759 (tp40) cc_final: 0.8480 (tm-30) REVERT: B 200 THR cc_start: 0.8631 (m) cc_final: 0.8405 (p) REVERT: C 170 LYS cc_start: 0.8551 (ttmm) cc_final: 0.8297 (ttpp) REVERT: C 179 GLN cc_start: 0.8735 (tp40) cc_final: 0.8384 (tp-100) REVERT: C 183 ASN cc_start: 0.8818 (m-40) cc_final: 0.8128 (m-40) REVERT: D 154 ARG cc_start: 0.8298 (mtt-85) cc_final: 0.8092 (mtt-85) REVERT: D 176 GLN cc_start: 0.6328 (pm20) cc_final: 0.6082 (pm20) REVERT: E 192 GLN cc_start: 0.8707 (tp40) cc_final: 0.8475 (tp40) REVERT: F 170 LYS cc_start: 0.8550 (ttmm) cc_final: 0.8235 (ttpp) REVERT: F 179 GLN cc_start: 0.8702 (tp40) cc_final: 0.8390 (tp-100) REVERT: F 182 LYS cc_start: 0.8678 (mttm) cc_final: 0.8430 (mttp) REVERT: F 183 ASN cc_start: 0.8857 (m-40) cc_final: 0.8205 (m-40) REVERT: F 195 ASN cc_start: 0.8201 (m-40) cc_final: 0.7960 (m110) REVERT: I 170 LYS cc_start: 0.8613 (ttmm) cc_final: 0.8338 (ttpp) REVERT: J 67 GLN cc_start: 0.8188 (tp40) cc_final: 0.7980 (tp40) REVERT: J 176 GLN cc_start: 0.6440 (pm20) cc_final: 0.5911 (pm20) REVERT: J 192 GLN cc_start: 0.8719 (tp40) cc_final: 0.8508 (tp40) REVERT: K 200 THR cc_start: 0.8809 (m) cc_final: 0.8581 (p) REVERT: L 179 GLN cc_start: 0.8856 (tp40) cc_final: 0.8593 (tp40) REVERT: L 183 ASN cc_start: 0.8758 (m-40) cc_final: 0.8443 (m-40) REVERT: L 195 ASN cc_start: 0.8379 (m-40) cc_final: 0.7901 (m110) REVERT: L 213 GLU cc_start: 0.8303 (mt-10) cc_final: 0.7868 (mt-10) REVERT: N 200 THR cc_start: 0.8773 (m) cc_final: 0.8500 (p) REVERT: O 183 ASN cc_start: 0.8931 (m-40) cc_final: 0.8719 (m-40) outliers start: 23 outliers final: 15 residues processed: 474 average time/residue: 0.3238 time to fit residues: 206.1244 Evaluate side-chains 462 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 447 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 HIS 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 198 CYS Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 120 HIS Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain O residue 212 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 136 optimal weight: 0.0000 chunk 76 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 overall best weight: 1.7790 ------------------------------------------------------------------------------- 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 I 195 ASN O 155 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14155 Z= 0.323 Angle : 0.627 11.002 19205 Z= 0.315 Chirality : 0.044 0.167 2185 Planarity : 0.005 0.040 2490 Dihedral : 4.413 18.992 1890 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.07 % Allowed : 15.40 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.19), residues: 1745 helix: 0.95 (0.14), residues: 1170 sheet: -2.68 (0.45), residues: 45 loop : 1.21 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 184 HIS 0.002 0.001 HIS G 12 PHE 0.012 0.001 PHE M 32 TYR 0.016 0.002 TYR G 145 ARG 0.005 0.001 ARG G 154 *********************** 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 fitting. rotamer outliers: 31 poor density : 461 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.8819 (tpt) cc_final: 0.8356 (tpt) REVERT: A 145 TYR cc_start: 0.8533 (m-80) cc_final: 0.8313 (m-80) REVERT: A 176 GLN cc_start: 0.6213 (pm20) cc_final: 0.5988 (pm20) REVERT: A 192 GLN cc_start: 0.8778 (tp40) cc_final: 0.8477 (tm-30) REVERT: B 200 THR cc_start: 0.8658 (m) cc_final: 0.8436 (p) REVERT: C 170 LYS cc_start: 0.8572 (ttmm) cc_final: 0.8321 (ttpp) REVERT: C 175 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7343 (mt-10) REVERT: C 179 GLN cc_start: 0.8752 (tp40) cc_final: 0.8410 (tp-100) REVERT: C 183 ASN cc_start: 0.8879 (m-40) cc_final: 0.8159 (m-40) REVERT: D 154 ARG cc_start: 0.8342 (mtt-85) cc_final: 0.8130 (mtt-85) REVERT: E 192 GLN cc_start: 0.8704 (tp40) cc_final: 0.8487 (tp40) REVERT: F 170 LYS cc_start: 0.8605 (ttmm) cc_final: 0.8288 (ttpp) REVERT: F 179 GLN cc_start: 0.8744 (tp40) cc_final: 0.8436 (tp-100) REVERT: F 182 LYS cc_start: 0.8712 (mttm) cc_final: 0.8502 (mttp) REVERT: F 183 ASN cc_start: 0.8817 (m-40) cc_final: 0.8076 (m-40) REVERT: F 195 ASN cc_start: 0.8237 (m-40) cc_final: 0.7980 (m110) REVERT: G 176 GLN cc_start: 0.6053 (pm20) cc_final: 0.5755 (pm20) REVERT: G 192 GLN cc_start: 0.8784 (tp40) cc_final: 0.8578 (tp40) REVERT: H 154 ARG cc_start: 0.8070 (mtt90) cc_final: 0.7833 (mmt-90) REVERT: H 179 GLN cc_start: 0.8711 (tp40) cc_final: 0.8395 (tp-100) REVERT: H 200 THR cc_start: 0.8775 (m) cc_final: 0.8522 (p) REVERT: I 166 ASP cc_start: 0.8224 (m-30) cc_final: 0.7780 (m-30) REVERT: I 170 LYS cc_start: 0.8623 (ttmm) cc_final: 0.8352 (ttpp) REVERT: J 33 SER cc_start: 0.8875 (t) cc_final: 0.8551 (m) REVERT: J 67 GLN cc_start: 0.8204 (tp40) cc_final: 0.7982 (tp40) REVERT: J 176 GLN cc_start: 0.6455 (pm20) cc_final: 0.5932 (pm20) REVERT: J 192 GLN cc_start: 0.8737 (tp40) cc_final: 0.8502 (tp40) REVERT: K 200 THR cc_start: 0.8844 (m) cc_final: 0.8608 (p) REVERT: L 179 GLN cc_start: 0.8835 (tp40) cc_final: 0.8612 (tp40) REVERT: L 183 ASN cc_start: 0.8750 (m-40) cc_final: 0.8508 (m-40) REVERT: L 195 ASN cc_start: 0.8384 (m-40) cc_final: 0.8018 (m-40) REVERT: L 213 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7910 (mt-10) REVERT: N 200 THR cc_start: 0.8843 (m) cc_final: 0.8583 (p) REVERT: O 183 ASN cc_start: 0.8877 (m-40) cc_final: 0.8551 (m110) outliers start: 31 outliers final: 22 residues processed: 475 average time/residue: 0.3322 time to fit residues: 212.2595 Evaluate side-chains 479 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 457 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 120 HIS 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 152 ASP Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain G residue 198 CYS Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain J residue 197 ASP Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 120 HIS Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain 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 158 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 138 optimal weight: 0.4980 chunk 91 optimal weight: 0.9980 chunk 163 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 75 optimal weight: 0.0870 chunk 101 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN G 50 GLN I 179 GLN I 183 ASN J 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14155 Z= 0.186 Angle : 0.582 10.373 19205 Z= 0.294 Chirality : 0.042 0.162 2185 Planarity : 0.005 0.040 2490 Dihedral : 4.237 18.285 1890 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.40 % Allowed : 16.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.19), residues: 1745 helix: 1.04 (0.15), residues: 1170 sheet: -2.46 (0.51), residues: 45 loop : 1.27 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 184 HIS 0.001 0.000 HIS A 12 PHE 0.010 0.001 PHE I 168 TYR 0.012 0.001 TYR L 164 ARG 0.007 0.001 ARG G 154 *********************** 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 492 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 471 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLN cc_start: 0.7940 (tm-30) cc_final: 0.7668 (tm-30) REVERT: A 50 GLN cc_start: 0.8250 (tt0) cc_final: 0.7913 (tt0) REVERT: A 66 MET cc_start: 0.8812 (tpt) cc_final: 0.8319 (tpt) REVERT: A 176 GLN cc_start: 0.6070 (pm20) cc_final: 0.5864 (pm20) REVERT: A 192 GLN cc_start: 0.8759 (tp40) cc_final: 0.8374 (tm-30) REVERT: B 179 GLN cc_start: 0.8512 (tp40) cc_final: 0.8084 (tp-100) REVERT: B 183 ASN cc_start: 0.8869 (m-40) cc_final: 0.8349 (m-40) REVERT: B 200 THR cc_start: 0.8643 (m) cc_final: 0.8430 (p) REVERT: C 170 LYS cc_start: 0.8524 (ttmm) cc_final: 0.8272 (ttpp) REVERT: C 183 ASN cc_start: 0.8749 (m-40) cc_final: 0.8355 (m-40) REVERT: D 154 ARG cc_start: 0.8296 (mtt-85) cc_final: 0.8075 (mtt-85) REVERT: E 192 GLN cc_start: 0.8692 (tp40) cc_final: 0.8489 (tp40) REVERT: F 170 LYS cc_start: 0.8537 (ttmm) cc_final: 0.8230 (ttpp) REVERT: F 179 GLN cc_start: 0.8752 (tp40) cc_final: 0.8467 (tp40) REVERT: F 183 ASN cc_start: 0.8754 (m-40) cc_final: 0.8232 (m-40) REVERT: F 195 ASN cc_start: 0.8255 (m-40) cc_final: 0.7957 (m110) REVERT: F 213 GLU cc_start: 0.8780 (mp0) cc_final: 0.8531 (pm20) REVERT: G 192 GLN cc_start: 0.8725 (tp40) cc_final: 0.8431 (tp40) REVERT: G 203 LYS cc_start: 0.8799 (mmtp) cc_final: 0.8596 (mmtp) REVERT: H 200 THR cc_start: 0.8720 (m) cc_final: 0.8482 (p) REVERT: I 170 LYS cc_start: 0.8589 (ttmm) cc_final: 0.8308 (ttpp) REVERT: I 179 GLN cc_start: 0.8947 (tp-100) cc_final: 0.8667 (tp-100) REVERT: I 183 ASN cc_start: 0.8883 (m110) cc_final: 0.8571 (m-40) REVERT: J 67 GLN cc_start: 0.8191 (tp40) cc_final: 0.7968 (tp40) REVERT: J 176 GLN cc_start: 0.6365 (pm20) cc_final: 0.5904 (pm20) REVERT: J 192 GLN cc_start: 0.8736 (tp40) cc_final: 0.8529 (tp40) REVERT: L 179 GLN cc_start: 0.8758 (tp40) cc_final: 0.8509 (tp40) REVERT: L 183 ASN cc_start: 0.8738 (m-40) cc_final: 0.8464 (m-40) REVERT: L 195 ASN cc_start: 0.8381 (m-40) cc_final: 0.7901 (m110) REVERT: L 213 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7867 (mt-10) REVERT: M 176 GLN cc_start: 0.6459 (pm20) cc_final: 0.5788 (pm20) REVERT: N 200 THR cc_start: 0.8722 (m) cc_final: 0.8480 (p) outliers start: 21 outliers final: 16 residues processed: 478 average time/residue: 0.3145 time to fit residues: 202.8092 Evaluate side-chains 466 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 450 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain D residue 120 HIS Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain G residue 198 CYS Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain M residue 120 HIS Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain O residue 159 GLU Chi-restraints excluded: chain O residue 205 LEU 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 65 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 128 optimal weight: 7.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 GLN ** D 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 GLN M 50 GLN O 179 GLN O 183 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14155 Z= 0.215 Angle : 0.599 10.752 19205 Z= 0.303 Chirality : 0.042 0.159 2185 Planarity : 0.005 0.039 2490 Dihedral : 4.236 19.996 1890 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.47 % Allowed : 16.60 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.19), residues: 1745 helix: 0.99 (0.15), residues: 1170 sheet: -2.59 (0.48), residues: 45 loop : 1.26 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 184 HIS 0.002 0.000 HIS A 12 PHE 0.008 0.001 PHE M 32 TYR 0.013 0.001 TYR O 169 ARG 0.007 0.001 ARG G 154 *********************** 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 482 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 460 time to evaluate : 1.772 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 13 GLN cc_start: 0.7883 (tm-30) cc_final: 0.7629 (tm-30) REVERT: A 50 GLN cc_start: 0.8291 (tt0) cc_final: 0.7960 (tt0) REVERT: A 66 MET cc_start: 0.8805 (tpt) cc_final: 0.8314 (tpt) REVERT: A 192 GLN cc_start: 0.8806 (tp40) cc_final: 0.8526 (tm-30) REVERT: B 200 THR cc_start: 0.8647 (m) cc_final: 0.8440 (p) REVERT: C 170 LYS cc_start: 0.8530 (ttmm) cc_final: 0.8279 (ttpp) REVERT: C 179 GLN cc_start: 0.8866 (tp40) cc_final: 0.8558 (tp40) REVERT: C 183 ASN cc_start: 0.8829 (m-40) cc_final: 0.8450 (m-40) REVERT: D 154 ARG cc_start: 0.8347 (mtt-85) cc_final: 0.8144 (mtt-85) REVERT: E 200 THR cc_start: 0.8631 (m) cc_final: 0.8413 (p) REVERT: F 170 LYS cc_start: 0.8585 (ttmm) cc_final: 0.8277 (ttpp) REVERT: F 183 ASN cc_start: 0.8775 (m-40) cc_final: 0.8171 (m-40) REVERT: F 195 ASN cc_start: 0.8276 (m-40) cc_final: 0.7981 (m110) REVERT: G 18 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8406 (mtm180) REVERT: G 203 LYS cc_start: 0.8779 (mmtp) cc_final: 0.8577 (mmtp) REVERT: H 200 THR cc_start: 0.8730 (m) cc_final: 0.8506 (p) REVERT: I 170 LYS cc_start: 0.8588 (ttmm) cc_final: 0.8302 (ttpp) REVERT: J 67 GLN cc_start: 0.8189 (tp40) cc_final: 0.7965 (tp40) REVERT: J 176 GLN cc_start: 0.6381 (pm20) cc_final: 0.5947 (pm20) REVERT: J 192 GLN cc_start: 0.8741 (tp40) cc_final: 0.8538 (tp40) REVERT: L 179 GLN cc_start: 0.8758 (tp40) cc_final: 0.8485 (tp40) REVERT: L 183 ASN cc_start: 0.8828 (m-40) cc_final: 0.8452 (m-40) REVERT: L 195 ASN cc_start: 0.8390 (m-40) cc_final: 0.7903 (m110) REVERT: L 213 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7866 (mt-10) REVERT: M 154 ARG cc_start: 0.8419 (mtt90) cc_final: 0.8133 (mtt90) REVERT: M 176 GLN cc_start: 0.6369 (pm20) cc_final: 0.5966 (pm20) REVERT: N 154 ARG cc_start: 0.8211 (mtt-85) cc_final: 0.8005 (mmt-90) REVERT: N 200 THR cc_start: 0.8736 (m) cc_final: 0.8494 (p) REVERT: O 212 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7899 (pm20) outliers start: 22 outliers final: 14 residues processed: 471 average time/residue: 0.3183 time to fit residues: 201.8416 Evaluate side-chains 469 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 453 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 HIS 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 18 ARG Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain G residue 198 CYS Chi-restraints excluded: chain H residue 153 ILE Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain M residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 119 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 144 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN F 179 GLN I 179 GLN K 179 GLN ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 179 GLN O 183 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14155 Z= 0.302 Angle : 0.653 11.792 19205 Z= 0.330 Chirality : 0.044 0.174 2185 Planarity : 0.005 0.039 2490 Dihedral : 4.407 21.079 1890 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.67 % Allowed : 16.33 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.19), residues: 1745 helix: 0.83 (0.15), residues: 1155 sheet: -2.68 (0.45), residues: 45 loop : 1.14 (0.23), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 184 HIS 0.002 0.001 HIS A 12 PHE 0.011 0.001 PHE M 32 TYR 0.011 0.001 TYR K 169 ARG 0.007 0.001 ARG G 132 *********************** 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 484 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 459 time to evaluate : 1.607 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: 0.8816 (tpt) cc_final: 0.8358 (tpt) REVERT: B 200 THR cc_start: 0.8667 (m) cc_final: 0.8456 (p) REVERT: C 170 LYS cc_start: 0.8544 (ttmm) cc_final: 0.8286 (ttpp) REVERT: C 183 ASN cc_start: 0.8950 (m-40) cc_final: 0.8637 (m-40) REVERT: D 154 ARG cc_start: 0.8353 (mtt-85) cc_final: 0.8147 (mtt-85) REVERT: F 170 LYS cc_start: 0.8616 (ttmm) cc_final: 0.8305 (ttpp) REVERT: F 179 GLN cc_start: 0.8834 (tp-100) cc_final: 0.8205 (tp40) REVERT: F 183 ASN cc_start: 0.8766 (m-40) cc_final: 0.8442 (m-40) REVERT: G 18 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8435 (mtm180) REVERT: G 176 GLN cc_start: 0.5624 (pm20) cc_final: 0.5114 (pm20) REVERT: G 192 GLN cc_start: 0.8722 (tp40) cc_final: 0.8510 (tp40) REVERT: G 203 LYS cc_start: 0.8771 (mmtp) cc_final: 0.8559 (mmtp) REVERT: I 170 LYS cc_start: 0.8606 (ttmm) cc_final: 0.8322 (ttpp) REVERT: J 67 GLN cc_start: 0.8190 (tp40) cc_final: 0.7977 (tp40) REVERT: J 176 GLN cc_start: 0.6512 (pm20) cc_final: 0.6057 (pm20) REVERT: J 192 GLN cc_start: 0.8740 (tp40) cc_final: 0.8509 (tp40) REVERT: L 179 GLN cc_start: 0.8829 (tp40) cc_final: 0.8602 (tp40) REVERT: L 183 ASN cc_start: 0.8827 (m-40) cc_final: 0.8516 (m-40) REVERT: L 195 ASN cc_start: 0.8389 (m-40) cc_final: 0.7905 (m110) REVERT: L 213 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7871 (mt-10) REVERT: M 176 GLN cc_start: 0.6320 (pm20) cc_final: 0.5953 (pm20) REVERT: N 200 THR cc_start: 0.8770 (m) cc_final: 0.8545 (p) REVERT: O 212 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7932 (pm20) outliers start: 25 outliers final: 16 residues processed: 471 average time/residue: 0.3186 time to fit residues: 202.4164 Evaluate side-chains 471 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 453 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 HIS 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 18 ARG Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain G residue 198 CYS Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain L residue 212 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 112 optimal weight: 0.4980 chunk 169 optimal weight: 0.6980 chunk 155 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 143 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 GLN I 179 GLN I 183 ASN J 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14155 Z= 0.197 Angle : 0.610 11.377 19205 Z= 0.311 Chirality : 0.042 0.183 2185 Planarity : 0.005 0.040 2490 Dihedral : 4.245 18.710 1890 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.20 % Allowed : 16.60 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.19), residues: 1745 helix: 0.93 (0.15), residues: 1170 sheet: -2.42 (0.51), residues: 45 loop : 1.17 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 184 HIS 0.001 0.000 HIS A 12 PHE 0.007 0.001 PHE E 168 TYR 0.017 0.001 TYR A 145 ARG 0.007 0.001 ARG J 132 ********************** 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 480 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 462 time to evaluate : 1.724 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 13 GLN cc_start: 0.7853 (tm-30) cc_final: 0.7617 (tm-30) REVERT: A 50 GLN cc_start: 0.8300 (tt0) cc_final: 0.7966 (tt0) REVERT: A 66 MET cc_start: 0.8798 (tpt) cc_final: 0.8322 (tpt) REVERT: A 192 GLN cc_start: 0.8800 (tp40) cc_final: 0.8422 (tm-30) REVERT: B 183 ASN cc_start: 0.8836 (m-40) cc_final: 0.8322 (m-40) REVERT: C 170 LYS cc_start: 0.8511 (ttmm) cc_final: 0.8241 (ttpp) REVERT: E 200 THR cc_start: 0.8627 (m) cc_final: 0.8418 (p) REVERT: F 170 LYS cc_start: 0.8595 (ttmm) cc_final: 0.8289 (ttpp) REVERT: G 176 GLN cc_start: 0.5353 (pm20) cc_final: 0.4807 (pm20) REVERT: I 170 LYS cc_start: 0.8592 (ttmm) cc_final: 0.8304 (ttpp) REVERT: J 67 GLN cc_start: 0.8180 (tp40) cc_final: 0.7961 (tp40) REVERT: J 192 GLN cc_start: 0.8741 (tp40) cc_final: 0.8536 (tp40) REVERT: K 179 GLN cc_start: 0.8481 (tp40) cc_final: 0.8183 (tp-100) REVERT: K 183 ASN cc_start: 0.8840 (m-40) cc_final: 0.8621 (m-40) REVERT: L 195 ASN cc_start: 0.8410 (m-40) cc_final: 0.8022 (m110) REVERT: L 213 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7850 (mt-10) REVERT: M 154 ARG cc_start: 0.8387 (mtt90) cc_final: 0.8108 (mtt90) REVERT: M 176 GLN cc_start: 0.6158 (pm20) cc_final: 0.5854 (pm20) REVERT: N 200 THR cc_start: 0.8774 (m) cc_final: 0.8541 (p) REVERT: O 212 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7896 (pm20) outliers start: 18 outliers final: 15 residues processed: 468 average time/residue: 0.3309 time to fit residues: 210.9173 Evaluate side-chains 461 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 445 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain D residue 120 HIS Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 218 CYS Chi-restraints excluded: chain G residue 120 HIS Chi-restraints excluded: chain G residue 198 CYS Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain J residue 120 HIS Chi-restraints excluded: chain L residue 212 GLU Chi-restraints excluded: chain 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 205 LEU 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: 1.9990 chunk 124 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 118 optimal weight: 0.0570 chunk 7 optimal weight: 3.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN F 179 GLN F 183 ASN G 50 GLN I 183 ASN ** N 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.138553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.107349 restraints weight = 21905.470| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.57 r_work: 0.3236 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14155 Z= 0.257 Angle : 0.635 9.851 19205 Z= 0.326 Chirality : 0.044 0.167 2185 Planarity : 0.005 0.043 2490 Dihedral : 4.350 20.025 1890 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.27 % Allowed : 17.33 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.19), residues: 1745 helix: 0.80 (0.15), residues: 1155 sheet: -2.54 (0.49), residues: 45 loop : 1.09 (0.23), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 184 HIS 0.002 0.000 HIS A 12 PHE 0.010 0.001 PHE M 32 TYR 0.018 0.001 TYR A 145 ARG 0.007 0.001 ARG G 132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4290.13 seconds wall clock time: 76 minutes 26.41 seconds (4586.41 seconds total)