Starting phenix.real_space_refine on Sun Mar 24 22:51:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4h_24826/03_2024/7s4h_24826_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4h_24826/03_2024/7s4h_24826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4h_24826/03_2024/7s4h_24826.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4h_24826/03_2024/7s4h_24826.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4h_24826/03_2024/7s4h_24826_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4h_24826/03_2024/7s4h_24826_trim_updated.pdb" } resolution = 2.14 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= 0.000 sd= 0.006 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 19395 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: 6 Type Number sf(0) Gaussians Cu 9 5.60 5 P 36 5.49 5 S 93 5.16 5 C 15030 2.51 5 N 3417 2.21 5 O 4304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 79": "OE1" <-> "OE2" Residue "A ASP 82": "OD1" <-> "OD2" Residue "A PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 160": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 328": "OD1" <-> "OD2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A ASP 378": "OD1" <-> "OD2" Residue "A ASP 406": "OD1" <-> "OD2" Residue "C TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 228": "OE1" <-> "OE2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C GLU 280": "OE1" <-> "OE2" Residue "B ASP 22": "OD1" <-> "OD2" Residue "B ASP 47": "OD1" <-> "OD2" Residue "F GLU 13": "OE1" <-> "OE2" Residue "F ASP 47": "OD1" <-> "OD2" Residue "F GLU 195": "OE1" <-> "OE2" Residue "F GLU 241": "OE1" <-> "OE2" Residue "J GLU 13": "OE1" <-> "OE2" Residue "J ASP 49": "OD1" <-> "OD2" Residue "J GLU 100": "OE1" <-> "OE2" Residue "J GLU 241": "OE1" <-> "OE2" Residue "E PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 79": "OE1" <-> "OE2" Residue "E ASP 82": "OD1" <-> "OD2" Residue "E PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 160": "OE1" <-> "OE2" Residue "E GLU 276": "OE1" <-> "OE2" Residue "E PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 328": "OD1" <-> "OD2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E GLU 343": "OE1" <-> "OE2" Residue "E ASP 368": "OD1" <-> "OD2" Residue "E ASP 378": "OD1" <-> "OD2" Residue "E ASP 406": "OD1" <-> "OD2" Residue "I PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 79": "OE1" <-> "OE2" Residue "I ASP 82": "OD1" <-> "OD2" Residue "I PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 160": "OE1" <-> "OE2" Residue "I GLU 276": "OE1" <-> "OE2" Residue "I PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 328": "OD1" <-> "OD2" Residue "I GLU 338": "OE1" <-> "OE2" Residue "I GLU 343": "OE1" <-> "OE2" Residue "I ASP 368": "OD1" <-> "OD2" Residue "I ASP 378": "OD1" <-> "OD2" Residue "I ASP 406": "OD1" <-> "OD2" Residue "G TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 84": "OE1" <-> "OE2" Residue "G PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 126": "OE1" <-> "OE2" Residue "G GLU 176": "OE1" <-> "OE2" Residue "G PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 228": "OE1" <-> "OE2" Residue "G GLU 237": "OE1" <-> "OE2" Residue "G GLU 280": "OE1" <-> "OE2" Residue "K TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 84": "OE1" <-> "OE2" Residue "K PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 126": "OE1" <-> "OE2" Residue "K GLU 176": "OE1" <-> "OE2" Residue "K PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 228": "OE1" <-> "OE2" Residue "K GLU 237": "OE1" <-> "OE2" Residue "K GLU 280": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22889 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "C" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1972 Classifications: {'peptide': 236} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain: "B" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1977 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "F" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1977 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "J" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1977 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "E" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "I" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "G" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1972 Classifications: {'peptide': 236} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain: "K" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1972 Classifications: {'peptide': 236} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' CU': 2, 'D10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 315 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 284 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "F" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 200 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "J" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 242 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' CU': 2, 'D10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' CU': 2, 'D10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 273 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "K" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 231 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "A" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "J" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "E" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "I" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Time building chain proxies: 11.46, per 1000 atoms: 0.50 Number of scatterers: 22889 At special positions: 0 Unit cell: (106.722, 106.722, 119, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cu 9 28.99 S 93 16.00 P 36 15.00 O 4304 8.00 N 3417 7.00 C 15030 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 - 3.50 Amino acid : False - 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: 9.29 Conformation dependent library (CDL) restraints added in 3.5 seconds 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4758 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 81 helices and 21 sheets defined 47.9% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.91 Creating SS restraints... Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 185 through 207 Processing helix chain 'A' and resid 213 through 220 Processing helix chain 'A' and resid 232 through 256 Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.546A pdb=" N ILE A 379 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 72 removed outlier: 3.940A pdb=" N TYR C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 88 removed outlier: 3.587A pdb=" N THR C 87 " --> pdb=" O PRO C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 113 Processing helix chain 'C' and resid 124 through 149 Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 171 through 176 Processing helix chain 'C' and resid 180 through 198 Processing helix chain 'C' and resid 208 through 232 Proline residue: C 217 - end of helix removed outlier: 3.548A pdb=" N ILE C 220 " --> pdb=" O GLY C 216 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU C 221 " --> pdb=" O PRO C 217 " (cutoff:3.500A) Proline residue: C 222 - end of helix removed outlier: 4.638A pdb=" N GLY C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU C 226 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 269 removed outlier: 4.438A pdb=" N GLY C 247 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE C 250 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE C 251 " --> pdb=" O PHE C 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 44 Processing helix chain 'B' and resid 46 through 50 Processing helix chain 'B' and resid 59 through 83 Proline residue: B 65 - end of helix removed outlier: 4.440A pdb=" N THR B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N PHE B 71 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Proline residue: B 72 - end of helix removed outlier: 3.992A pdb=" N GLU B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 106 Processing helix chain 'B' and resid 116 through 119 No H-bonds generated for 'chain 'B' and resid 116 through 119' Processing helix chain 'B' and resid 125 through 136 Processing helix chain 'B' and resid 141 through 168 removed outlier: 4.107A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE B 156 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N TYR B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Proline residue: B 158 - end of helix Proline residue: B 162 - end of helix Proline residue: B 166 - end of helix Processing helix chain 'B' and resid 180 through 187 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 212 through 238 removed outlier: 3.750A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 44 Processing helix chain 'F' and resid 46 through 50 Processing helix chain 'F' and resid 59 through 83 Proline residue: F 65 - end of helix removed outlier: 4.435A pdb=" N THR F 70 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N PHE F 71 " --> pdb=" O VAL F 67 " (cutoff:3.500A) Proline residue: F 72 - end of helix removed outlier: 3.990A pdb=" N GLU F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 106 Processing helix chain 'F' and resid 116 through 119 No H-bonds generated for 'chain 'F' and resid 116 through 119' Processing helix chain 'F' and resid 125 through 136 Processing helix chain 'F' and resid 141 through 168 removed outlier: 4.115A pdb=" N ALA F 149 " --> pdb=" O ALA F 145 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE F 156 " --> pdb=" O TRP F 152 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N TYR F 157 " --> pdb=" O GLY F 153 " (cutoff:3.500A) Proline residue: F 158 - end of helix Proline residue: F 162 - end of helix Proline residue: F 166 - end of helix Processing helix chain 'F' and resid 180 through 187 Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 212 through 238 removed outlier: 3.750A pdb=" N PHE F 233 " --> pdb=" O PHE F 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 44 Processing helix chain 'J' and resid 46 through 50 Processing helix chain 'J' and resid 59 through 83 Proline residue: J 65 - end of helix removed outlier: 4.440A pdb=" N THR J 70 " --> pdb=" O ILE J 66 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N PHE J 71 " --> pdb=" O VAL J 67 " (cutoff:3.500A) Proline residue: J 72 - end of helix removed outlier: 3.994A pdb=" N GLU J 81 " --> pdb=" O SER J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 106 Processing helix chain 'J' and resid 116 through 119 No H-bonds generated for 'chain 'J' and resid 116 through 119' Processing helix chain 'J' and resid 125 through 136 Processing helix chain 'J' and resid 141 through 168 removed outlier: 4.113A pdb=" N ALA J 149 " --> pdb=" O ALA J 145 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE J 156 " --> pdb=" O TRP J 152 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N TYR J 157 " --> pdb=" O GLY J 153 " (cutoff:3.500A) Proline residue: J 158 - end of helix Proline residue: J 162 - end of helix Proline residue: J 166 - end of helix Processing helix chain 'J' and resid 180 through 187 Processing helix chain 'J' and resid 195 through 197 No H-bonds generated for 'chain 'J' and resid 195 through 197' Processing helix chain 'J' and resid 212 through 239 removed outlier: 3.798A pdb=" N PHE J 233 " --> pdb=" O PHE J 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 44 Processing helix chain 'E' and resid 163 through 165 No H-bonds generated for 'chain 'E' and resid 163 through 165' Processing helix chain 'E' and resid 185 through 207 Processing helix chain 'E' and resid 213 through 220 Processing helix chain 'E' and resid 232 through 256 Processing helix chain 'E' and resid 338 through 340 No H-bonds generated for 'chain 'E' and resid 338 through 340' Processing helix chain 'E' and resid 369 through 373 Processing helix chain 'E' and resid 376 through 381 removed outlier: 3.545A pdb=" N ILE E 379 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE E 380 " --> pdb=" O SER E 377 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 44 Processing helix chain 'I' and resid 163 through 165 No H-bonds generated for 'chain 'I' and resid 163 through 165' Processing helix chain 'I' and resid 185 through 207 Processing helix chain 'I' and resid 213 through 220 Processing helix chain 'I' and resid 232 through 256 Processing helix chain 'I' and resid 338 through 340 No H-bonds generated for 'chain 'I' and resid 338 through 340' Processing helix chain 'I' and resid 369 through 373 Processing helix chain 'I' and resid 376 through 381 removed outlier: 3.547A pdb=" N ILE I 379 " --> pdb=" O LEU I 376 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE I 380 " --> pdb=" O SER I 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 72 removed outlier: 3.940A pdb=" N TYR G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 88 removed outlier: 3.587A pdb=" N THR G 87 " --> pdb=" O PRO G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 113 Processing helix chain 'G' and resid 124 through 149 Processing helix chain 'G' and resid 151 through 162 Processing helix chain 'G' and resid 171 through 176 Processing helix chain 'G' and resid 180 through 198 Processing helix chain 'G' and resid 208 through 232 Proline residue: G 217 - end of helix removed outlier: 3.547A pdb=" N ILE G 220 " --> pdb=" O GLY G 216 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU G 221 " --> pdb=" O PRO G 217 " (cutoff:3.500A) Proline residue: G 222 - end of helix removed outlier: 4.638A pdb=" N GLY G 225 " --> pdb=" O LEU G 221 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU G 226 " --> pdb=" O PRO G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 269 removed outlier: 4.439A pdb=" N GLY G 247 " --> pdb=" O LEU G 244 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE G 250 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE G 251 " --> pdb=" O PHE G 248 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 72 removed outlier: 3.940A pdb=" N TYR K 58 " --> pdb=" O ALA K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 88 removed outlier: 3.587A pdb=" N THR K 87 " --> pdb=" O PRO K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 113 Processing helix chain 'K' and resid 124 through 149 Processing helix chain 'K' and resid 151 through 162 Processing helix chain 'K' and resid 171 through 176 Processing helix chain 'K' and resid 180 through 198 Processing helix chain 'K' and resid 208 through 232 Proline residue: K 217 - end of helix removed outlier: 3.547A pdb=" N ILE K 220 " --> pdb=" O GLY K 216 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU K 221 " --> pdb=" O PRO K 217 " (cutoff:3.500A) Proline residue: K 222 - end of helix removed outlier: 4.638A pdb=" N GLY K 225 " --> pdb=" O LEU K 221 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU K 226 " --> pdb=" O PRO K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 243 through 269 removed outlier: 4.438A pdb=" N GLY K 247 " --> pdb=" O LEU K 244 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE K 250 " --> pdb=" O GLY K 247 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE K 251 " --> pdb=" O PHE K 248 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 47 through 50 removed outlier: 6.671A pdb=" N LYS A 129 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ARG A 100 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 58 through 60 removed outlier: 8.391A pdb=" N VAL A 59 " --> pdb=" O TRP A 156 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N THR A 158 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 141 through 144 Processing sheet with id= D, first strand: chain 'A' and resid 169 through 171 Processing sheet with id= E, first strand: chain 'A' and resid 409 through 412 removed outlier: 9.602A pdb=" N ILE A 410 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA A 289 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N SER A 412 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N TYR A 291 " --> pdb=" O SER A 412 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ALA A 289 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG A 299 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N TYR A 291 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ALA A 297 " --> pdb=" O TYR A 291 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 323 through 325 removed outlier: 6.573A pdb=" N PHE A 392 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE A 317 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU A 390 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 170 through 173 Processing sheet with id= H, first strand: chain 'F' and resid 170 through 173 Processing sheet with id= I, first strand: chain 'J' and resid 170 through 173 Processing sheet with id= J, first strand: chain 'E' and resid 47 through 50 removed outlier: 6.672A pdb=" N LYS E 129 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ARG E 100 " --> pdb=" O LYS E 129 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 58 through 60 removed outlier: 8.391A pdb=" N VAL E 59 " --> pdb=" O TRP E 156 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N THR E 158 " --> pdb=" O VAL E 59 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 141 through 144 Processing sheet with id= M, first strand: chain 'E' and resid 169 through 171 Processing sheet with id= N, first strand: chain 'E' and resid 409 through 412 removed outlier: 9.602A pdb=" N ILE E 410 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA E 289 " --> pdb=" O ILE E 410 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N SER E 412 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N TYR E 291 " --> pdb=" O SER E 412 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ALA E 289 " --> pdb=" O ARG E 299 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG E 299 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N TYR E 291 " --> pdb=" O ALA E 297 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ALA E 297 " --> pdb=" O TYR E 291 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 323 through 325 removed outlier: 6.573A pdb=" N PHE E 392 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE E 317 " --> pdb=" O LEU E 390 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU E 390 " --> pdb=" O PHE E 317 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 47 through 50 removed outlier: 6.671A pdb=" N LYS I 129 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ARG I 100 " --> pdb=" O LYS I 129 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 58 through 60 removed outlier: 8.391A pdb=" N VAL I 59 " --> pdb=" O TRP I 156 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N THR I 158 " --> pdb=" O VAL I 59 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 141 through 144 Processing sheet with id= S, first strand: chain 'I' and resid 169 through 171 Processing sheet with id= T, first strand: chain 'I' and resid 409 through 412 removed outlier: 9.602A pdb=" N ILE I 410 " --> pdb=" O GLU I 287 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA I 289 " --> pdb=" O ILE I 410 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N SER I 412 " --> pdb=" O ALA I 289 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N TYR I 291 " --> pdb=" O SER I 412 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ALA I 289 " --> pdb=" O ARG I 299 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG I 299 " --> pdb=" O ALA I 289 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N TYR I 291 " --> pdb=" O ALA I 297 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ALA I 297 " --> pdb=" O TYR I 291 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 323 through 325 removed outlier: 6.573A pdb=" N PHE I 392 " --> pdb=" O GLY I 315 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE I 317 " --> pdb=" O LEU I 390 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU I 390 " --> pdb=" O PHE I 317 " (cutoff:3.500A) 1012 hydrogen bonds defined for protein. 2793 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: 6.79 Time building geometry restraints manager: 9.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3390 1.32 - 1.44: 6724 1.44 - 1.57: 12700 1.57 - 1.69: 133 1.69 - 1.81: 180 Bond restraints: 23127 Sorted by residual: bond pdb=" CB PLC C 310 " pdb=" O3 PLC C 310 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" CB PLC G 301 " pdb=" O3 PLC G 301 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" CB PLC F 302 " pdb=" O3 PLC F 302 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" CB PLC B 301 " pdb=" O3 PLC B 301 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" CB PLC J 302 " pdb=" O3 PLC J 302 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.01e+01 ... (remaining 23122 not shown) Histogram of bond angle deviations from ideal: 98.02 - 105.89: 567 105.89 - 113.75: 12983 113.75 - 121.62: 12867 121.62 - 129.48: 4570 129.48 - 137.35: 306 Bond angle restraints: 31293 Sorted by residual: angle pdb=" C HIS K 173 " pdb=" CA HIS K 173 " pdb=" CB HIS K 173 " ideal model delta sigma weight residual 110.85 98.59 12.26 1.70e+00 3.46e-01 5.20e+01 angle pdb=" C9' PLC F 302 " pdb=" CA' PLC F 302 " pdb=" CB' PLC F 302 " ideal model delta sigma weight residual 112.96 134.58 -21.62 3.00e+00 1.11e-01 5.20e+01 angle pdb=" C9' PLC B 301 " pdb=" CA' PLC B 301 " pdb=" CB' PLC B 301 " ideal model delta sigma weight residual 112.96 134.58 -21.62 3.00e+00 1.11e-01 5.19e+01 angle pdb=" C HIS C 173 " pdb=" CA HIS C 173 " pdb=" CB HIS C 173 " ideal model delta sigma weight residual 110.85 98.60 12.25 1.70e+00 3.46e-01 5.19e+01 angle pdb=" C9' PLC J 302 " pdb=" CA' PLC J 302 " pdb=" CB' PLC J 302 " ideal model delta sigma weight residual 112.96 134.57 -21.61 3.00e+00 1.11e-01 5.19e+01 ... (remaining 31288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.45: 12629 34.45 - 68.91: 761 68.91 - 103.36: 101 103.36 - 137.81: 30 137.81 - 172.27: 24 Dihedral angle restraints: 13545 sinusoidal: 6093 harmonic: 7452 Sorted by residual: dihedral pdb=" C HIS K 173 " pdb=" N HIS K 173 " pdb=" CA HIS K 173 " pdb=" CB HIS K 173 " ideal model delta harmonic sigma weight residual -122.60 -109.35 -13.25 0 2.50e+00 1.60e-01 2.81e+01 dihedral pdb=" C HIS C 173 " pdb=" N HIS C 173 " pdb=" CA HIS C 173 " pdb=" CB HIS C 173 " ideal model delta harmonic sigma weight residual -122.60 -109.39 -13.21 0 2.50e+00 1.60e-01 2.79e+01 dihedral pdb=" C HIS G 173 " pdb=" N HIS G 173 " pdb=" CA HIS G 173 " pdb=" CB HIS G 173 " ideal model delta harmonic sigma weight residual -122.60 -109.43 -13.17 0 2.50e+00 1.60e-01 2.78e+01 ... (remaining 13542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2491 0.056 - 0.111: 597 0.111 - 0.167: 91 0.167 - 0.222: 19 0.222 - 0.278: 9 Chirality restraints: 3207 Sorted by residual: chirality pdb=" CA HIS K 173 " pdb=" N HIS K 173 " pdb=" C HIS K 173 " pdb=" CB HIS K 173 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA HIS C 173 " pdb=" N HIS C 173 " pdb=" C HIS C 173 " pdb=" CB HIS C 173 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA HIS G 173 " pdb=" N HIS G 173 " pdb=" C HIS G 173 " pdb=" CB HIS G 173 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 3204 not shown) Planarity restraints: 3732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP C 234 " -0.021 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C TRP C 234 " 0.073 2.00e-02 2.50e+03 pdb=" O TRP C 234 " -0.027 2.00e-02 2.50e+03 pdb=" N PHE C 235 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP G 234 " -0.021 2.00e-02 2.50e+03 4.21e-02 1.77e+01 pdb=" C TRP G 234 " 0.073 2.00e-02 2.50e+03 pdb=" O TRP G 234 " -0.027 2.00e-02 2.50e+03 pdb=" N PHE G 235 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP K 234 " -0.021 2.00e-02 2.50e+03 4.21e-02 1.77e+01 pdb=" C TRP K 234 " 0.073 2.00e-02 2.50e+03 pdb=" O TRP K 234 " -0.027 2.00e-02 2.50e+03 pdb=" N PHE K 235 " -0.025 2.00e-02 2.50e+03 ... (remaining 3729 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 21 2.18 - 2.86: 8468 2.86 - 3.54: 34552 3.54 - 4.22: 64825 4.22 - 4.90: 106969 Nonbonded interactions: 214835 Sorted by model distance: nonbonded pdb=" NE2 HIS K 245 " pdb="CU CU K 302 " model vdw 1.502 2.320 nonbonded pdb=" NE2 HIS C 245 " pdb="CU CU C 301 " model vdw 1.503 2.320 nonbonded pdb=" NE2 HIS G 245 " pdb="CU CU G 302 " model vdw 1.503 2.320 nonbonded pdb=" NE2 HIS C 231 " pdb="CU CU C 301 " model vdw 1.997 2.320 nonbonded pdb=" NE2 HIS K 231 " pdb="CU CU K 302 " model vdw 1.997 2.320 ... (remaining 214830 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 414 or resid 502)) selection = (chain 'E' and (resid 33 through 414 or resid 502)) selection = (chain 'I' and (resid 33 through 414 or resid 502)) } ncs_group { reference = (chain 'B' and (resid 7 through 247 or resid 304 through 306)) selection = (chain 'F' and (resid 7 through 247 or resid 304 through 306)) selection = (chain 'J' and (resid 7 through 247 or resid 304 through 306)) } ncs_group { reference = (chain 'C' and (resid 45 through 280 or resid 303 through 304 or resid 308)) selection = (chain 'G' and (resid 45 through 280 or resid 303 through 304 or resid 308)) selection = (chain 'K' and (resid 45 through 280 or resid 303 through 304 or resid 308)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.230 Construct map_model_manager: 0.020 Extract box with map and model: 17.610 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 57.550 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.180 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:11.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 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 : 0.009 0.127 23127 Z= 0.511 Angle : 1.029 21.624 31293 Z= 0.502 Chirality : 0.051 0.278 3207 Planarity : 0.005 0.045 3732 Dihedral : 22.825 172.265 8787 Min Nonbonded Distance : 1.502 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.85 % Favored : 94.92 % Rotamer: Outliers : 2.83 % Allowed : 17.60 % Favored : 79.56 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.71 (0.17), residues: 2559 helix: 0.86 (0.15), residues: 1230 sheet: 1.31 (0.28), residues: 357 loop : -0.22 (0.21), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 152 HIS 0.009 0.001 HIS K 173 PHE 0.017 0.002 PHE B 31 TYR 0.022 0.002 TYR K 184 ARG 0.005 0.001 ARG K 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 235 time to evaluate : 2.488 Fit side-chains REVERT: A 399 ASN cc_start: 0.7641 (p0) cc_final: 0.7244 (p0) REVERT: F 18 SER cc_start: 0.8937 (OUTLIER) cc_final: 0.8730 (t) REVERT: E 399 ASN cc_start: 0.7661 (p0) cc_final: 0.7269 (p0) REVERT: I 108 GLN cc_start: 0.8029 (pt0) cc_final: 0.7678 (pp30) REVERT: I 399 ASN cc_start: 0.7612 (p0) cc_final: 0.7198 (p0) REVERT: G 86 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7281 (tp30) REVERT: G 117 ARG cc_start: 0.8077 (mmt-90) cc_final: 0.7696 (mpt180) REVERT: K 117 ARG cc_start: 0.8078 (mmt-90) cc_final: 0.7752 (mpt180) outliers start: 62 outliers final: 30 residues processed: 288 average time/residue: 1.4678 time to fit residues: 479.1679 Evaluate side-chains 249 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 218 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 18 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 138 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 207 SER Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 207 SER Chi-restraints excluded: chain K residue 240 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 215 optimal weight: 6.9990 chunk 193 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 199 optimal weight: 7.9990 chunk 77 optimal weight: 0.1980 chunk 121 optimal weight: 4.9990 chunk 148 optimal weight: 8.9990 chunk 231 optimal weight: 4.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN G 161 GLN K 161 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.0667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23127 Z= 0.239 Angle : 0.624 6.725 31293 Z= 0.322 Chirality : 0.047 0.314 3207 Planarity : 0.005 0.037 3732 Dihedral : 22.824 179.957 4191 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.42 % Favored : 95.23 % Rotamer: Outliers : 3.43 % Allowed : 17.15 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.83 (0.17), residues: 2559 helix: 0.99 (0.15), residues: 1245 sheet: 1.25 (0.27), residues: 372 loop : -0.22 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 206 HIS 0.004 0.001 HIS A 192 PHE 0.020 0.002 PHE B 31 TYR 0.022 0.002 TYR G 184 ARG 0.003 0.000 ARG J 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 219 time to evaluate : 2.447 Fit side-chains REVERT: A 108 GLN cc_start: 0.8059 (pt0) cc_final: 0.7736 (pp30) REVERT: A 112 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8433 (mtm180) REVERT: A 208 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7447 (mtp180) REVERT: A 399 ASN cc_start: 0.7645 (p0) cc_final: 0.7240 (p0) REVERT: F 18 SER cc_start: 0.8992 (OUTLIER) cc_final: 0.8682 (t) REVERT: E 108 GLN cc_start: 0.7997 (pt0) cc_final: 0.7747 (pp30) REVERT: E 112 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8394 (mtt180) REVERT: E 399 ASN cc_start: 0.7688 (p0) cc_final: 0.7259 (p0) REVERT: I 108 GLN cc_start: 0.8035 (pt0) cc_final: 0.7719 (pp30) REVERT: I 112 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8351 (mtt180) REVERT: I 208 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7420 (mtp180) REVERT: I 399 ASN cc_start: 0.7647 (p0) cc_final: 0.7222 (p0) REVERT: G 86 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7235 (tp30) outliers start: 75 outliers final: 36 residues processed: 277 average time/residue: 1.5494 time to fit residues: 484.4777 Evaluate side-chains 258 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 216 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 18 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 138 SER Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 208 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 414 MET Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 158 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 231 optimal weight: 1.9990 chunk 250 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 chunk 230 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 186 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 160 HIS C 161 GLN F 187 ASN E 168 ASN I 176 GLN G 160 HIS G 161 GLN K 160 HIS K 161 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23127 Z= 0.286 Angle : 0.638 7.092 31293 Z= 0.334 Chirality : 0.048 0.250 3207 Planarity : 0.005 0.037 3732 Dihedral : 21.791 178.840 4178 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.88 % Favored : 94.76 % Rotamer: Outliers : 4.16 % Allowed : 16.00 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.82 (0.17), residues: 2559 helix: 0.98 (0.15), residues: 1227 sheet: 1.26 (0.27), residues: 369 loop : -0.19 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 231 HIS 0.006 0.001 HIS G 173 PHE 0.021 0.002 PHE B 31 TYR 0.023 0.002 TYR G 184 ARG 0.003 0.000 ARG K 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 230 time to evaluate : 2.484 Fit side-chains REVERT: A 112 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8456 (mtm180) REVERT: A 208 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7416 (mtp180) REVERT: A 399 ASN cc_start: 0.7640 (p0) cc_final: 0.7234 (p0) REVERT: B 198 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8053 (ttp-170) REVERT: F 198 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8371 (ttp-170) REVERT: J 13 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8083 (tt0) REVERT: J 198 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.7668 (ttp-170) REVERT: E 108 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7800 (pp30) REVERT: E 112 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8432 (mtt180) REVERT: E 399 ASN cc_start: 0.7630 (p0) cc_final: 0.7230 (p0) REVERT: I 108 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7690 (pp30) REVERT: I 112 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8386 (mtt180) REVERT: I 399 ASN cc_start: 0.7600 (p0) cc_final: 0.7172 (p0) outliers start: 91 outliers final: 40 residues processed: 297 average time/residue: 1.5523 time to fit residues: 520.3581 Evaluate side-chains 269 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 219 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 198 ARG Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 273 LYS Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 108 GLN Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 176 GLN Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 414 MET Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 214 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 229 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 232 optimal weight: 0.3980 chunk 246 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 220 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN F 187 ASN E 168 ASN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 161 GLN K 161 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23127 Z= 0.223 Angle : 0.593 7.504 31293 Z= 0.307 Chirality : 0.047 0.254 3207 Planarity : 0.004 0.038 3732 Dihedral : 21.242 179.491 4174 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.49 % Favored : 95.15 % Rotamer: Outliers : 3.52 % Allowed : 17.06 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.86 (0.17), residues: 2559 helix: 1.00 (0.15), residues: 1248 sheet: 1.08 (0.26), residues: 384 loop : -0.11 (0.21), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 206 HIS 0.003 0.001 HIS E 192 PHE 0.019 0.002 PHE B 31 TYR 0.021 0.002 TYR G 184 ARG 0.002 0.000 ARG K 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 233 time to evaluate : 2.435 Fit side-chains REVERT: A 108 GLN cc_start: 0.8049 (pt0) cc_final: 0.7668 (pp30) REVERT: A 112 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8410 (mtm180) REVERT: A 208 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7410 (mtp180) REVERT: A 399 ASN cc_start: 0.7616 (p0) cc_final: 0.7191 (p0) REVERT: B 198 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8323 (ttp-170) REVERT: F 198 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8396 (ttp-170) REVERT: J 198 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.7641 (ttp-170) REVERT: E 108 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7698 (pp30) REVERT: E 112 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8384 (mtt180) REVERT: E 208 ARG cc_start: 0.7803 (mtp180) cc_final: 0.7519 (mtt180) REVERT: E 399 ASN cc_start: 0.7620 (p0) cc_final: 0.7212 (p0) REVERT: I 108 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7713 (pp30) REVERT: I 112 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8332 (mtt180) REVERT: I 399 ASN cc_start: 0.7588 (p0) cc_final: 0.7151 (p0) REVERT: G 86 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7234 (tp30) outliers start: 77 outliers final: 42 residues processed: 295 average time/residue: 1.5183 time to fit residues: 506.9578 Evaluate side-chains 272 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 221 time to evaluate : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 198 ARG Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 108 GLN Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain I residue 414 MET Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 263 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 205 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 210 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 221 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN F 187 ASN E 168 ASN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 161 GLN K 161 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23127 Z= 0.265 Angle : 0.613 8.200 31293 Z= 0.319 Chirality : 0.047 0.264 3207 Planarity : 0.005 0.039 3732 Dihedral : 21.114 179.298 4174 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.85 % Favored : 94.80 % Rotamer: Outliers : 3.43 % Allowed : 16.92 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.85 (0.17), residues: 2559 helix: 0.98 (0.15), residues: 1239 sheet: 1.10 (0.26), residues: 384 loop : -0.09 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 231 HIS 0.004 0.001 HIS E 192 PHE 0.021 0.002 PHE B 31 TYR 0.022 0.002 TYR G 184 ARG 0.002 0.000 ARG K 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 225 time to evaluate : 2.669 Fit side-chains REVERT: A 108 GLN cc_start: 0.8072 (pt0) cc_final: 0.7736 (pp30) REVERT: A 112 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8445 (mtm180) REVERT: A 208 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7418 (mtp180) REVERT: A 399 ASN cc_start: 0.7605 (p0) cc_final: 0.7182 (p0) REVERT: B 198 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8159 (ttp-170) REVERT: F 198 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8368 (ttp-170) REVERT: J 198 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.7543 (ttp-170) REVERT: E 108 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7752 (pp30) REVERT: E 112 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8408 (mtt180) REVERT: E 208 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7526 (mtt180) REVERT: E 399 ASN cc_start: 0.7605 (p0) cc_final: 0.7197 (p0) REVERT: I 108 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7727 (pp30) REVERT: I 112 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8372 (mtt180) REVERT: I 208 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7530 (mtp180) REVERT: I 363 ASP cc_start: 0.7786 (m-30) cc_final: 0.7554 (m-30) REVERT: I 399 ASN cc_start: 0.7565 (p0) cc_final: 0.7135 (p0) outliers start: 75 outliers final: 47 residues processed: 284 average time/residue: 1.5308 time to fit residues: 491.2606 Evaluate side-chains 279 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 221 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 198 ARG Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 108 GLN Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 208 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain I residue 414 MET Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 263 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 82 optimal weight: 10.0000 chunk 221 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 144 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 246 optimal weight: 10.0000 chunk 204 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN F 187 ASN E 168 ASN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 GLN G 161 GLN K 161 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 23127 Z= 0.477 Angle : 0.752 10.064 31293 Z= 0.392 Chirality : 0.053 0.289 3207 Planarity : 0.006 0.046 3732 Dihedral : 22.161 174.363 4174 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.77 % Favored : 94.76 % Rotamer: Outliers : 3.66 % Allowed : 16.28 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.71 (0.17), residues: 2559 helix: 0.82 (0.15), residues: 1221 sheet: 1.33 (0.27), residues: 369 loop : -0.19 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J 231 HIS 0.007 0.002 HIS E 192 PHE 0.025 0.003 PHE F 31 TYR 0.024 0.003 TYR B 188 ARG 0.004 0.001 ARG E 375 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 224 time to evaluate : 2.357 Fit side-chains REVERT: A 108 GLN cc_start: 0.8120 (pt0) cc_final: 0.7830 (pp30) REVERT: A 112 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8491 (mtm180) REVERT: A 399 ASN cc_start: 0.7580 (p0) cc_final: 0.7127 (p0) REVERT: B 198 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.7319 (ttp-170) REVERT: F 198 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8388 (ttp-170) REVERT: J 198 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.7497 (ttp-170) REVERT: E 108 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7824 (pp30) REVERT: E 112 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8513 (mtt180) REVERT: E 208 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7499 (mtp180) REVERT: E 399 ASN cc_start: 0.7597 (p0) cc_final: 0.7170 (p0) REVERT: I 108 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7749 (pp30) REVERT: I 112 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8476 (mtt180) REVERT: I 208 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7530 (mtp180) REVERT: I 363 ASP cc_start: 0.7800 (m-30) cc_final: 0.7561 (m-30) REVERT: I 399 ASN cc_start: 0.7546 (p0) cc_final: 0.7101 (p0) outliers start: 80 outliers final: 45 residues processed: 284 average time/residue: 1.5428 time to fit residues: 492.4738 Evaluate side-chains 270 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 215 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 198 ARG Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 108 GLN Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 176 GLN Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 208 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 113 LYS Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 263 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 237 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 245 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN C 161 GLN B 187 ASN F 187 ASN E 168 ASN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 161 GLN K 161 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23127 Z= 0.201 Angle : 0.595 7.970 31293 Z= 0.308 Chirality : 0.046 0.257 3207 Planarity : 0.004 0.039 3732 Dihedral : 21.189 178.829 4168 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.73 % Favored : 95.15 % Rotamer: Outliers : 3.02 % Allowed : 17.15 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.85 (0.17), residues: 2559 helix: 0.95 (0.15), residues: 1242 sheet: 1.22 (0.27), residues: 369 loop : -0.08 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 74 HIS 0.003 0.001 HIS A 139 PHE 0.018 0.001 PHE B 31 TYR 0.020 0.001 TYR C 184 ARG 0.003 0.000 ARG C 115 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 225 time to evaluate : 2.435 Fit side-chains REVERT: A 108 GLN cc_start: 0.8041 (pt0) cc_final: 0.7764 (pp30) REVERT: A 112 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8406 (mtm180) REVERT: A 208 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7423 (mtp180) REVERT: A 399 ASN cc_start: 0.7598 (p0) cc_final: 0.7165 (p0) REVERT: E 108 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7728 (pp30) REVERT: E 112 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8370 (mtt180) REVERT: E 208 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7524 (mtt180) REVERT: E 399 ASN cc_start: 0.7606 (p0) cc_final: 0.7196 (p0) REVERT: I 108 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7689 (pp30) REVERT: I 112 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8313 (mtt180) REVERT: I 208 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7529 (mtp180) REVERT: I 363 ASP cc_start: 0.7764 (m-30) cc_final: 0.7513 (m-30) outliers start: 66 outliers final: 33 residues processed: 278 average time/residue: 1.4869 time to fit residues: 465.6772 Evaluate side-chains 260 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 219 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 108 GLN Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 208 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 263 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 152 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 146 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 156 optimal weight: 10.0000 chunk 167 optimal weight: 0.9980 chunk 121 optimal weight: 9.9990 chunk 22 optimal weight: 0.5980 chunk 193 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN C 161 GLN F 187 ASN E 168 ASN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 161 GLN K 161 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23127 Z= 0.194 Angle : 0.577 7.653 31293 Z= 0.299 Chirality : 0.046 0.248 3207 Planarity : 0.004 0.038 3732 Dihedral : 20.316 179.803 4168 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.73 % Favored : 95.04 % Rotamer: Outliers : 2.70 % Allowed : 17.51 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.93 (0.17), residues: 2559 helix: 1.00 (0.15), residues: 1245 sheet: 1.18 (0.27), residues: 369 loop : 0.03 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 74 HIS 0.003 0.001 HIS I 192 PHE 0.018 0.001 PHE B 31 TYR 0.021 0.001 TYR G 184 ARG 0.006 0.000 ARG J 84 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 221 time to evaluate : 2.329 Fit side-chains REVERT: A 108 GLN cc_start: 0.8025 (pt0) cc_final: 0.7747 (pp30) REVERT: A 112 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8422 (mtm180) REVERT: A 208 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7411 (mtp180) REVERT: E 108 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7725 (pp30) REVERT: E 112 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8371 (mtt180) REVERT: E 208 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7498 (mtt180) REVERT: E 399 ASN cc_start: 0.7588 (p0) cc_final: 0.7195 (p0) REVERT: I 108 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7693 (pp30) REVERT: I 112 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8327 (mtt180) REVERT: I 208 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7520 (mtp180) REVERT: I 363 ASP cc_start: 0.7767 (m-30) cc_final: 0.7520 (m-30) outliers start: 59 outliers final: 34 residues processed: 271 average time/residue: 1.5883 time to fit residues: 483.4132 Evaluate side-chains 261 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 219 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 108 GLN Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 208 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 263 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 223 optimal weight: 10.0000 chunk 235 optimal weight: 9.9990 chunk 214 optimal weight: 4.9990 chunk 229 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 179 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 206 optimal weight: 9.9990 chunk 216 optimal weight: 0.9990 chunk 228 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN C 161 GLN F 187 ASN J 187 ASN E 168 ASN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN I 176 GLN G 161 GLN K 161 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 23127 Z= 0.345 Angle : 0.671 8.656 31293 Z= 0.350 Chirality : 0.050 0.254 3207 Planarity : 0.005 0.039 3732 Dihedral : 20.516 177.610 4165 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.96 % Favored : 94.69 % Rotamer: Outliers : 2.33 % Allowed : 18.02 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.89 (0.17), residues: 2559 helix: 0.93 (0.15), residues: 1221 sheet: 1.35 (0.27), residues: 354 loop : 0.01 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 74 HIS 0.005 0.001 HIS E 192 PHE 0.024 0.002 PHE B 31 TYR 0.023 0.002 TYR G 184 ARG 0.003 0.000 ARG J 198 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 224 time to evaluate : 2.573 Fit side-chains REVERT: A 108 GLN cc_start: 0.8105 (pt0) cc_final: 0.7818 (pp30) REVERT: A 112 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8473 (mtm180) REVERT: E 108 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7836 (pp30) REVERT: E 112 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8453 (mtt180) REVERT: E 208 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7548 (mtt180) REVERT: E 399 ASN cc_start: 0.7556 (p0) cc_final: 0.7138 (p0) REVERT: I 108 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7740 (pp30) REVERT: I 112 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8419 (mtt180) REVERT: I 208 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7533 (mtp180) REVERT: I 363 ASP cc_start: 0.7792 (m-30) cc_final: 0.7547 (m-30) outliers start: 51 outliers final: 36 residues processed: 266 average time/residue: 1.6033 time to fit residues: 479.1245 Evaluate side-chains 266 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 223 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 176 GLN Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 108 GLN Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 176 GLN Chi-restraints excluded: chain I residue 208 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 263 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 150 optimal weight: 5.9990 chunk 242 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 254 optimal weight: 4.9990 chunk 233 optimal weight: 2.9990 chunk 202 optimal weight: 20.0000 chunk 21 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN F 187 ASN E 168 ASN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 161 GLN K 161 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23127 Z= 0.269 Angle : 0.635 8.440 31293 Z= 0.330 Chirality : 0.048 0.250 3207 Planarity : 0.005 0.038 3732 Dihedral : 20.220 177.847 4165 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.88 % Favored : 95.00 % Rotamer: Outliers : 2.19 % Allowed : 18.20 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.86 (0.17), residues: 2559 helix: 0.92 (0.15), residues: 1239 sheet: 1.12 (0.27), residues: 369 loop : 0.04 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K 74 HIS 0.004 0.001 HIS E 192 PHE 0.020 0.002 PHE B 31 TYR 0.022 0.002 TYR G 184 ARG 0.003 0.000 ARG K 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 220 time to evaluate : 2.509 Fit side-chains REVERT: A 108 GLN cc_start: 0.8083 (pt0) cc_final: 0.7792 (pp30) REVERT: A 112 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8424 (mtm180) REVERT: E 108 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7748 (pp30) REVERT: E 112 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8409 (mtt180) REVERT: E 208 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7549 (mtt180) REVERT: I 108 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7720 (pp30) REVERT: I 112 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8360 (mtt180) REVERT: I 208 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7538 (mtp180) REVERT: I 363 ASP cc_start: 0.7775 (m-30) cc_final: 0.7531 (m-30) outliers start: 48 outliers final: 36 residues processed: 261 average time/residue: 1.6304 time to fit residues: 478.2928 Evaluate side-chains 262 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 219 time to evaluate : 2.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 108 GLN Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 208 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 263 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 160 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 186 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 202 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 GLN G 161 GLN K 161 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.118271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.093679 restraints weight = 24047.553| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.21 r_work: 0.2975 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 23127 Z= 0.367 Angle : 0.690 8.850 31293 Z= 0.360 Chirality : 0.050 0.251 3207 Planarity : 0.005 0.039 3732 Dihedral : 20.374 175.513 4165 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.04 % Favored : 94.61 % Rotamer: Outliers : 2.24 % Allowed : 18.29 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % 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: 0.83 (0.17), residues: 2559 helix: 0.88 (0.15), residues: 1221 sheet: 1.35 (0.27), residues: 354 loop : -0.03 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP K 74 HIS 0.006 0.001 HIS A 192 PHE 0.024 0.002 PHE B 31 TYR 0.023 0.002 TYR G 184 ARG 0.003 0.000 ARG A 375 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8508.24 seconds wall clock time: 155 minutes 30.50 seconds (9330.50 seconds total)