Starting phenix.real_space_refine on Sun Mar 24 22:31:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4j_24828/03_2024/7s4j_24828_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4j_24828/03_2024/7s4j_24828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4j_24828/03_2024/7s4j_24828.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4j_24828/03_2024/7s4j_24828.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4j_24828/03_2024/7s4j_24828_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4j_24828/03_2024/7s4j_24828_trim_updated.pdb" } resolution = 2.16 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= 0.005 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 19419 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 4195 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 288": "OD1" <-> "OD2" Residue "C TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 288": "OD1" <-> "OD2" Residue "I ASP 288": "OD1" <-> "OD2" Residue "G TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22780 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: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1976 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 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: "F" Number of atoms: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1976 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "J" Number of atoms: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1976 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 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: 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: "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: 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: "K" 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: "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: 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: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "E" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "I" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Chain: "G" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "F" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "J" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Time building chain proxies: 12.77, per 1000 atoms: 0.56 Number of scatterers: 22780 At special positions: 0 Unit cell: (107.194, 108.139, 118.528, 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 4195 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: 10.47 Conformation dependent library (CDL) restraints added in 4.2 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: 78 helices and 24 sheets defined 47.5% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.48 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: 3.547A pdb=" N ILE A 379 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 72 removed outlier: 3.986A pdb=" N TYR C 58 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 88 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 161 removed outlier: 3.614A pdb=" N GLN C 161 " --> pdb=" O GLY C 157 " (cutoff:3.500A) 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: 4.351A pdb=" N LEU C 221 " --> pdb=" O PRO C 217 " (cutoff:3.500A) Proline residue: C 222 - end of helix removed outlier: 4.774A pdb=" N GLY C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU C 226 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 269 removed outlier: 4.350A 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) Processing helix chain 'B' and resid 11 through 42 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: 4.396A pdb=" N THR B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N PHE B 71 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Proline residue: B 72 - end of helix removed outlier: 3.932A 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: 4.217A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE B 156 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 5.117A 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 209 through 238 removed outlier: 3.855A pdb=" N VAL B 212 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Proline residue: B 214 - end of helix removed outlier: 3.522A pdb=" N MET B 223 " --> pdb=" O SER B 220 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS B 232 " --> pdb=" O PHE B 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: 3.547A pdb=" N ILE E 379 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 3.668A 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: 3.668A pdb=" N ILE I 380 " --> pdb=" O SER I 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 72 removed outlier: 3.987A pdb=" N TYR G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 88 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 161 removed outlier: 3.614A pdb=" N GLN G 161 " --> pdb=" O GLY G 157 " (cutoff:3.500A) 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: 3.548A pdb=" N ILE G 220 " --> pdb=" O GLY G 216 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU G 221 " --> pdb=" O PRO G 217 " (cutoff:3.500A) Proline residue: G 222 - end of helix removed outlier: 4.773A pdb=" N GLY G 225 " --> pdb=" O LEU G 221 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU G 226 " --> pdb=" O PRO G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 269 removed outlier: 4.350A pdb=" N GLY G 247 " --> pdb=" O LEU G 244 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE G 250 " --> pdb=" O GLY G 247 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 72 removed outlier: 3.986A pdb=" N TYR K 58 " --> pdb=" O ALA K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 88 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 161 removed outlier: 3.614A pdb=" N GLN K 161 " --> pdb=" O GLY K 157 " (cutoff:3.500A) 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: 4.351A pdb=" N LEU K 221 " --> pdb=" O PRO K 217 " (cutoff:3.500A) Proline residue: K 222 - end of helix removed outlier: 4.775A pdb=" N GLY K 225 " --> pdb=" O LEU K 221 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU K 226 " --> pdb=" O PRO K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 243 through 269 removed outlier: 4.351A pdb=" N GLY K 247 " --> pdb=" O LEU K 244 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE K 250 " --> pdb=" O GLY K 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 42 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: 4.396A pdb=" N THR F 70 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N PHE F 71 " --> pdb=" O VAL F 67 " (cutoff:3.500A) Proline residue: F 72 - end of helix removed outlier: 3.931A 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: 4.217A pdb=" N ALA F 149 " --> pdb=" O ALA F 145 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE F 156 " --> pdb=" O TRP F 152 " (cutoff:3.500A) removed outlier: 5.117A 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 209 through 238 removed outlier: 3.854A pdb=" N VAL F 212 " --> pdb=" O GLY F 209 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA F 213 " --> pdb=" O LYS F 210 " (cutoff:3.500A) Proline residue: F 214 - end of helix removed outlier: 3.521A pdb=" N MET F 223 " --> pdb=" O SER F 220 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS F 232 " --> pdb=" O PHE F 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 42 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: 4.395A pdb=" N THR J 70 " --> pdb=" O ILE J 66 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N PHE J 71 " --> pdb=" O VAL J 67 " (cutoff:3.500A) Proline residue: J 72 - end of helix removed outlier: 3.932A 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: 4.217A pdb=" N ALA J 149 " --> pdb=" O ALA J 145 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE J 156 " --> pdb=" O TRP J 152 " (cutoff:3.500A) removed outlier: 5.117A 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 209 through 238 removed outlier: 3.855A pdb=" N VAL J 212 " --> pdb=" O GLY J 209 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA J 213 " --> pdb=" O LYS J 210 " (cutoff:3.500A) Proline residue: J 214 - end of helix removed outlier: 3.522A pdb=" N MET J 223 " --> pdb=" O SER J 220 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS J 232 " --> pdb=" O PHE J 229 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 47 through 50 removed outlier: 6.638A pdb=" N LYS A 129 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 5.730A 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: 8.444A pdb=" N VAL A 59 " --> pdb=" O TRP A 156 " (cutoff:3.500A) removed outlier: 6.290A 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 282 through 286 Processing sheet with id= F, first strand: chain 'A' and resid 298 through 300 removed outlier: 6.326A pdb=" N ILE A 410 " --> pdb=" O TYR A 291 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 323 through 325 removed outlier: 6.579A pdb=" N PHE A 392 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE A 317 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 390 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 170 through 173 Processing sheet with id= I, first strand: chain 'E' and resid 47 through 50 removed outlier: 6.638A pdb=" N LYS E 129 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ARG E 100 " --> pdb=" O LYS E 129 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 58 through 60 removed outlier: 8.444A pdb=" N VAL E 59 " --> pdb=" O TRP E 156 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N THR E 158 " --> pdb=" O VAL E 59 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 141 through 144 Processing sheet with id= L, first strand: chain 'E' and resid 169 through 171 Processing sheet with id= M, first strand: chain 'E' and resid 282 through 286 Processing sheet with id= N, first strand: chain 'E' and resid 298 through 300 removed outlier: 6.326A pdb=" N ILE E 410 " --> pdb=" O TYR E 291 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 323 through 325 removed outlier: 6.579A pdb=" N PHE E 392 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE E 317 " --> pdb=" O LEU E 390 " (cutoff:3.500A) removed outlier: 6.489A 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: 6.638A pdb=" N LYS I 129 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 5.730A 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: 8.444A pdb=" N VAL I 59 " --> pdb=" O TRP I 156 " (cutoff:3.500A) removed outlier: 6.290A 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 282 through 286 Processing sheet with id= U, first strand: chain 'I' and resid 298 through 300 removed outlier: 6.326A pdb=" N ILE I 410 " --> pdb=" O TYR I 291 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 323 through 325 removed outlier: 6.579A pdb=" N PHE I 392 " --> pdb=" O GLY I 315 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE I 317 " --> pdb=" O LEU I 390 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU I 390 " --> pdb=" O PHE I 317 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 170 through 173 Processing sheet with id= X, first strand: chain 'J' and resid 170 through 173 999 hydrogen bonds defined for protein. 2565 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: 11.13 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: 3288 1.32 - 1.44: 6821 1.44 - 1.56: 12706 1.56 - 1.69: 129 1.69 - 1.81: 180 Bond restraints: 23124 Sorted by residual: 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 4.03e+01 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 4.02e+01 bond pdb=" CB PLC J 303 " pdb=" O3 PLC J 303 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.02e+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 ... (remaining 23119 not shown) Histogram of bond angle deviations from ideal: 97.29 - 104.79: 474 104.79 - 112.29: 11659 112.29 - 119.79: 8304 119.79 - 127.29: 10442 127.29 - 134.79: 408 Bond angle restraints: 31287 Sorted by residual: angle pdb=" C9' PLC F 302 " pdb=" CA' PLC F 302 " pdb=" CB' PLC F 302 " ideal model delta sigma weight residual 112.96 134.59 -21.63 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=" C9' PLC J 303 " pdb=" CA' PLC J 303 " pdb=" CB' PLC J 303 " ideal model delta sigma weight residual 112.96 134.58 -21.62 3.00e+00 1.11e-01 5.19e+01 angle pdb=" CA HIS G 160 " pdb=" CB HIS G 160 " pdb=" CG HIS G 160 " ideal model delta sigma weight residual 113.80 106.85 6.95 1.00e+00 1.00e+00 4.83e+01 angle pdb=" CA HIS C 160 " pdb=" CB HIS C 160 " pdb=" CG HIS C 160 " ideal model delta sigma weight residual 113.80 106.86 6.94 1.00e+00 1.00e+00 4.82e+01 ... (remaining 31282 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.45: 12528 34.45 - 68.90: 870 68.90 - 103.35: 93 103.35 - 137.81: 36 137.81 - 172.26: 18 Dihedral angle restraints: 13545 sinusoidal: 6093 harmonic: 7452 Sorted by residual: dihedral pdb=" CA GLN J 245 " pdb=" C GLN J 245 " pdb=" N SER J 246 " pdb=" CA SER J 246 " ideal model delta harmonic sigma weight residual 180.00 153.02 26.98 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA GLN B 245 " pdb=" C GLN B 245 " pdb=" N SER B 246 " pdb=" CA SER B 246 " ideal model delta harmonic sigma weight residual 180.00 153.03 26.97 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA GLN F 245 " pdb=" C GLN F 245 " pdb=" N SER F 246 " pdb=" CA SER F 246 " ideal model delta harmonic sigma weight residual 180.00 153.06 26.94 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 13542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2368 0.054 - 0.108: 682 0.108 - 0.162: 124 0.162 - 0.216: 24 0.216 - 0.270: 9 Chirality restraints: 3207 Sorted by residual: chirality pdb=" CA ILE K 174 " pdb=" N ILE K 174 " pdb=" C ILE K 174 " pdb=" CB ILE K 174 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA ILE G 174 " pdb=" N ILE G 174 " pdb=" C ILE G 174 " pdb=" CB ILE G 174 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA ILE C 174 " pdb=" N ILE C 174 " pdb=" C ILE C 174 " pdb=" CB ILE C 174 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 3204 not shown) Planarity restraints: 3729 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS K 173 " -0.017 2.00e-02 2.50e+03 2.08e-02 6.51e+00 pdb=" CG HIS K 173 " -0.002 2.00e-02 2.50e+03 pdb=" ND1 HIS K 173 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 HIS K 173 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 HIS K 173 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS K 173 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 173 " -0.017 2.00e-02 2.50e+03 2.08e-02 6.48e+00 pdb=" CG HIS C 173 " -0.001 2.00e-02 2.50e+03 pdb=" ND1 HIS C 173 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 HIS C 173 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 HIS C 173 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS C 173 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS G 173 " -0.017 2.00e-02 2.50e+03 2.07e-02 6.42e+00 pdb=" CG HIS G 173 " -0.001 2.00e-02 2.50e+03 pdb=" ND1 HIS G 173 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 HIS G 173 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 HIS G 173 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS G 173 " -0.030 2.00e-02 2.50e+03 ... (remaining 3726 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 222 2.54 - 3.13: 17416 3.13 - 3.72: 38949 3.72 - 4.31: 59759 4.31 - 4.90: 93981 Nonbonded interactions: 210327 Sorted by model distance: nonbonded pdb=" ND1 HIS A 48 " pdb="CU CU A 502 " model vdw 1.948 2.320 nonbonded pdb=" ND1 HIS I 48 " pdb="CU CU I 502 " model vdw 1.948 2.320 nonbonded pdb=" ND1 HIS E 48 " pdb="CU CU E 502 " model vdw 1.949 2.320 nonbonded pdb=" ND1 HIS E 72 " pdb="CU CU E 502 " model vdw 1.971 2.320 nonbonded pdb=" ND1 HIS A 72 " pdb="CU CU A 502 " model vdw 1.972 2.320 ... (remaining 210322 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' selection = chain 'E' selection = chain 'I' } ncs_group { reference = (chain 'B' and (resid 7 through 247 or resid 305 through 306)) selection = (chain 'F' and (resid 7 through 247 or resid 305 through 306)) selection = (chain 'J' and (resid 7 through 247 or resid 305 through 306)) } ncs_group { reference = (chain 'C' and (resid 45 through 280 or resid 309)) selection = (chain 'G' and (resid 45 through 280 or resid 309)) selection = (chain 'K' and (resid 45 through 280 or resid 309)) } 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: 3.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.250 Construct map_model_manager: 0.020 Extract box with map and model: 18.820 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 64.260 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.170 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:11.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 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 23124 Z= 0.561 Angle : 1.074 21.629 31287 Z= 0.527 Chirality : 0.054 0.270 3207 Planarity : 0.005 0.041 3729 Dihedral : 22.909 172.257 8787 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.51 % Allowed : 5.16 % Favored : 94.33 % Rotamer: Outliers : 4.30 % Allowed : 18.88 % Favored : 76.82 % Cbeta Deviations : 0.04 % 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: 0.65 (0.17), residues: 2559 helix: 0.91 (0.15), residues: 1242 sheet: 0.35 (0.27), residues: 405 loop : -0.01 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 206 HIS 0.026 0.002 HIS K 173 PHE 0.021 0.002 PHE F 31 TYR 0.022 0.002 TYR K 184 ARG 0.009 0.001 ARG C 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 359 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 265 time to evaluate : 2.463 Fit side-chains TARDY: cannot create tardy model for: "GLN B 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 245 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 288 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7593 (p0) REVERT: B 47 ASP cc_start: 0.7419 (m-30) cc_final: 0.7216 (m-30) REVERT: E 245 LEU cc_start: 0.8822 (mm) cc_final: 0.8548 (tt) REVERT: I 245 LEU cc_start: 0.8809 (mm) cc_final: 0.8548 (tt) REVERT: G 116 ASP cc_start: 0.8398 (t70) cc_final: 0.7922 (t0) REVERT: G 119 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8709 (mt) REVERT: K 233 PHE cc_start: 0.7508 (t80) cc_final: 0.7303 (t80) REVERT: F 113 TYR cc_start: 0.8360 (m-80) cc_final: 0.8132 (m-80) REVERT: F 150 MET cc_start: 0.7894 (tpt) cc_final: 0.7493 (tpt) outliers start: 94 outliers final: 47 residues processed: 340 average time/residue: 1.4479 time to fit residues: 557.5223 Evaluate side-chains 299 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 250 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 211 ASP Chi-restraints excluded: chain J residue 244 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 215 optimal weight: 0.9990 chunk 193 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 199 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 176 GLN I 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23124 Z= 0.198 Angle : 0.615 7.341 31287 Z= 0.314 Chirality : 0.046 0.316 3207 Planarity : 0.005 0.041 3729 Dihedral : 22.647 175.896 4228 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.96 % Favored : 94.88 % Rotamer: Outliers : 4.53 % Allowed : 17.65 % Favored : 77.82 % 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: 0.66 (0.17), residues: 2559 helix: 0.86 (0.15), residues: 1242 sheet: 0.66 (0.27), residues: 396 loop : -0.06 (0.22), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 206 HIS 0.004 0.001 HIS B 168 PHE 0.018 0.001 PHE B 31 TYR 0.021 0.001 TYR K 184 ARG 0.007 0.000 ARG K 117 *********************** 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 362 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 263 time to evaluate : 2.467 Fit side-chains TARDY: cannot create tardy model for: "GLN B 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 112 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8676 (mtt90) REVERT: E 112 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8704 (mtt90) REVERT: E 299 ARG cc_start: 0.7667 (ttp80) cc_final: 0.7409 (ttp80) REVERT: I 112 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8522 (mtt90) REVERT: I 245 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8540 (tt) REVERT: G 116 ASP cc_start: 0.8356 (t70) cc_final: 0.7870 (t0) REVERT: F 113 TYR cc_start: 0.8292 (m-80) cc_final: 0.8075 (m-80) outliers start: 99 outliers final: 45 residues processed: 339 average time/residue: 1.5313 time to fit residues: 584.3558 Evaluate side-chains 295 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 246 time to evaluate : 2.573 ------------------------------------------------------------------------------- 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 80 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 292 ARG Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 397 THR 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 80 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 292 ARG Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 414 MET Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 192 optimal weight: 10.0000 chunk 157 optimal weight: 0.5980 chunk 63 optimal weight: 6.9990 chunk 231 optimal weight: 4.9990 chunk 250 optimal weight: 0.9980 chunk 206 optimal weight: 10.0000 chunk 230 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 186 optimal weight: 10.0000 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN ** C 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 GLN I 176 GLN I 401 GLN G 223 ASN ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 231 HIS ** K 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 23124 Z= 0.318 Angle : 0.660 7.563 31287 Z= 0.342 Chirality : 0.049 0.279 3207 Planarity : 0.005 0.044 3729 Dihedral : 21.608 179.033 4198 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.69 % Favored : 95.04 % Rotamer: Outliers : 4.48 % Allowed : 17.47 % Favored : 78.05 % 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: 0.52 (0.16), residues: 2559 helix: 0.66 (0.14), residues: 1233 sheet: 0.59 (0.26), residues: 393 loop : 0.02 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 231 HIS 0.009 0.001 HIS B 168 PHE 0.022 0.002 PHE G 248 TYR 0.024 0.002 TYR K 184 ARG 0.009 0.000 ARG C 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 355 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 257 time to evaluate : 2.519 Fit side-chains TARDY: cannot create tardy model for: "GLN B 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 112 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.7583 (mtt90) REVERT: A 145 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7246 (tp40) REVERT: E 112 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8490 (mtt90) REVERT: E 145 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8061 (tt0) REVERT: E 245 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8536 (tt) REVERT: E 287 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.7043 (mm-30) REVERT: E 288 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7953 (p0) REVERT: I 112 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.7780 (mtt90) REVERT: I 245 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8551 (tt) REVERT: G 116 ASP cc_start: 0.8389 (t70) cc_final: 0.7861 (t0) REVERT: K 63 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8910 (mp) outliers start: 98 outliers final: 51 residues processed: 327 average time/residue: 1.5001 time to fit residues: 553.9841 Evaluate side-chains 305 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 244 time to evaluate : 2.484 ------------------------------------------------------------------------------- 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 80 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 145 GLN Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 287 GLU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 292 ARG Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 397 THR 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 80 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 292 ARG Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 414 MET Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 211 ASP Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 93 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 229 optimal weight: 7.9990 chunk 174 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 232 optimal weight: 8.9990 chunk 246 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 220 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN ** B 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 GLN I 145 GLN I 176 GLN I 401 GLN G 223 ASN G 276 GLN K 223 ASN ** K 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 276 GLN ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 23124 Z= 0.300 Angle : 0.643 7.641 31287 Z= 0.334 Chirality : 0.048 0.288 3207 Planarity : 0.005 0.044 3729 Dihedral : 20.728 179.818 4190 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.61 % Favored : 95.15 % Rotamer: Outliers : 4.07 % Allowed : 17.60 % Favored : 78.33 % 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: 0.51 (0.16), residues: 2559 helix: 0.68 (0.14), residues: 1227 sheet: 0.56 (0.26), residues: 393 loop : -0.03 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 231 HIS 0.007 0.001 HIS B 168 PHE 0.032 0.002 PHE C 248 TYR 0.022 0.002 TYR K 184 ARG 0.011 0.001 ARG C 117 *********************** 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 351 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 262 time to evaluate : 2.347 Fit side-chains TARDY: cannot create tardy model for: "GLN B 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 403 VAL cc_start: 0.9253 (OUTLIER) cc_final: 0.9039 (p) REVERT: E 102 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8159 (mt-10) REVERT: E 112 ARG cc_start: 0.9111 (OUTLIER) cc_final: 0.7246 (mtt90) REVERT: E 145 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.8038 (tt0) REVERT: E 245 LEU cc_start: 0.8818 (mp) cc_final: 0.8527 (tt) REVERT: E 287 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7135 (mm-30) REVERT: E 288 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.8001 (p0) REVERT: I 112 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.7273 (mtt90) REVERT: I 245 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8557 (tt) REVERT: I 288 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7922 (p0) REVERT: F 47 ASP cc_start: 0.7305 (m-30) cc_final: 0.7032 (m-30) REVERT: F 150 MET cc_start: 0.7959 (tpt) cc_final: 0.7512 (tpt) outliers start: 89 outliers final: 52 residues processed: 321 average time/residue: 1.4937 time to fit residues: 541.0272 Evaluate side-chains 310 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 249 time to evaluate : 2.882 ------------------------------------------------------------------------------- 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 141 MET Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 145 GLN Chi-restraints excluded: chain E residue 287 GLU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 292 ARG Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 359 THR 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 80 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 145 GLN Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 292 ARG Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 414 MET Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 241 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 205 optimal weight: 0.8980 chunk 139 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 210 optimal weight: 6.9990 chunk 170 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 221 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 GLN I 401 GLN G 223 ASN ** K 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 23124 Z= 0.399 Angle : 0.699 7.836 31287 Z= 0.363 Chirality : 0.051 0.292 3207 Planarity : 0.005 0.046 3729 Dihedral : 20.671 179.781 4180 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.96 % Favored : 94.80 % Rotamer: Outliers : 4.57 % Allowed : 16.42 % Favored : 79.01 % 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: 0.42 (0.16), residues: 2559 helix: 0.58 (0.14), residues: 1233 sheet: 0.46 (0.26), residues: 393 loop : -0.01 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 231 HIS 0.011 0.001 HIS B 168 PHE 0.032 0.002 PHE C 248 TYR 0.022 0.002 TYR K 146 ARG 0.007 0.001 ARG G 117 *********************** 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 353 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 253 time to evaluate : 2.573 Fit side-chains TARDY: cannot create tardy model for: "GLN B 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 112 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.7586 (mtt90) REVERT: A 145 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7222 (tp40) REVERT: B 137 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8390 (mt) REVERT: E 145 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8148 (tt0) REVERT: E 245 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8548 (tt) REVERT: E 287 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7184 (mm-30) REVERT: E 288 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.8014 (p0) REVERT: I 145 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.7403 (tp40) REVERT: I 245 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8560 (tt) REVERT: I 288 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7977 (p0) REVERT: K 63 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9052 (mp) REVERT: K 279 CYS cc_start: 0.6041 (OUTLIER) cc_final: 0.5747 (p) REVERT: F 13 GLU cc_start: 0.8395 (tt0) cc_final: 0.8182 (tt0) REVERT: F 137 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8291 (mt) outliers start: 100 outliers final: 52 residues processed: 322 average time/residue: 1.4999 time to fit residues: 544.5554 Evaluate side-chains 314 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 249 time to evaluate : 2.456 ------------------------------------------------------------------------------- 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 141 MET Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 145 GLN Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 287 GLU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 292 ARG Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 397 THR 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 145 GLN Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 292 ARG Chi-restraints excluded: chain I residue 298 MET Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 414 MET Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 279 CYS Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 241 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 82 optimal weight: 1.9990 chunk 221 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 246 optimal weight: 1.9990 chunk 204 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN E 176 GLN I 145 GLN I 168 ASN I 401 GLN G 161 GLN G 223 ASN ** K 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23124 Z= 0.192 Angle : 0.590 7.746 31287 Z= 0.304 Chirality : 0.046 0.276 3207 Planarity : 0.004 0.051 3729 Dihedral : 19.848 176.975 4171 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.85 % Favored : 95.04 % Rotamer: Outliers : 3.38 % Allowed : 17.79 % Favored : 78.83 % 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: 0.55 (0.16), residues: 2559 helix: 0.75 (0.15), residues: 1233 sheet: 0.60 (0.26), residues: 390 loop : -0.08 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 231 HIS 0.003 0.001 HIS E 139 PHE 0.031 0.001 PHE C 248 TYR 0.021 0.001 TYR C 184 ARG 0.006 0.000 ARG K 117 *********************** 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 334 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 260 time to evaluate : 2.398 Fit side-chains TARDY: cannot create tardy model for: "GLN B 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 112 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.7406 (mtt90) REVERT: A 145 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7153 (tp40) REVERT: A 245 LEU cc_start: 0.8833 (mm) cc_final: 0.8526 (tt) REVERT: E 45 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7361 (mtp85) REVERT: E 145 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.8013 (tt0) REVERT: E 245 LEU cc_start: 0.8814 (mp) cc_final: 0.8524 (tt) REVERT: I 145 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8172 (tt0) REVERT: I 245 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8541 (tt) REVERT: I 288 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7920 (p0) REVERT: G 214 VAL cc_start: 0.8816 (OUTLIER) cc_final: 0.8530 (p) REVERT: K 63 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9050 (mp) REVERT: F 47 ASP cc_start: 0.7315 (m-30) cc_final: 0.7058 (m-30) REVERT: F 150 MET cc_start: 0.7917 (tpt) cc_final: 0.7557 (tpt) outliers start: 74 outliers final: 42 residues processed: 313 average time/residue: 1.5254 time to fit residues: 540.6362 Evaluate side-chains 304 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 253 time to evaluate : 2.744 ------------------------------------------------------------------------------- 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 145 GLN Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 145 GLN Chi-restraints excluded: chain E residue 292 ARG Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 414 MET 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 145 GLN Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 292 ARG Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 414 MET Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain K residue 63 LEU Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 241 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 237 optimal weight: 0.2980 chunk 27 optimal weight: 0.0000 chunk 140 optimal weight: 0.8980 chunk 180 optimal weight: 30.0000 chunk 139 optimal weight: 0.8980 chunk 207 optimal weight: 0.3980 chunk 137 optimal weight: 0.9990 chunk 245 optimal weight: 8.9990 chunk 153 optimal weight: 0.3980 chunk 149 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN E 168 ASN E 176 GLN I 168 ASN G 161 GLN G 223 ASN ** K 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 ASN J 187 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 23124 Z= 0.139 Angle : 0.553 8.297 31287 Z= 0.282 Chirality : 0.044 0.263 3207 Planarity : 0.004 0.055 3729 Dihedral : 18.995 179.833 4169 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.69 % Favored : 95.19 % Rotamer: Outliers : 2.93 % Allowed : 18.43 % Favored : 78.65 % 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: 0.71 (0.17), residues: 2559 helix: 0.89 (0.15), residues: 1224 sheet: 0.78 (0.26), residues: 390 loop : -0.07 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 202 HIS 0.003 0.001 HIS J 232 PHE 0.031 0.001 PHE C 248 TYR 0.020 0.001 TYR C 184 ARG 0.010 0.000 ARG G 117 *********************** 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 324 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 260 time to evaluate : 2.321 Fit side-chains TARDY: cannot create tardy model for: "GLN B 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 45 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7474 (mtp85) REVERT: A 112 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.7550 (mtt90) REVERT: E 45 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7719 (mtp85) REVERT: E 145 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7995 (tt0) REVERT: E 245 LEU cc_start: 0.8813 (mp) cc_final: 0.8495 (tt) REVERT: I 45 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7578 (mtp85) REVERT: I 245 LEU cc_start: 0.8795 (mm) cc_final: 0.8519 (tt) REVERT: G 116 ASP cc_start: 0.8315 (t70) cc_final: 0.7732 (t0) REVERT: G 154 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7858 (tt0) REVERT: F 150 MET cc_start: 0.7862 (tpt) cc_final: 0.7589 (tpt) outliers start: 64 outliers final: 34 residues processed: 307 average time/residue: 1.4638 time to fit residues: 506.7957 Evaluate side-chains 285 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 245 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ARG 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 292 ARG Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 145 GLN Chi-restraints excluded: chain E residue 292 ARG Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 292 ARG Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 241 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 152 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 156 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 193 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN E 168 ASN E 176 GLN ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 23124 Z= 0.357 Angle : 0.683 8.469 31287 Z= 0.353 Chirality : 0.050 0.271 3207 Planarity : 0.005 0.054 3729 Dihedral : 19.299 179.975 4164 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.92 % Favored : 94.80 % Rotamer: Outliers : 3.02 % Allowed : 18.20 % Favored : 78.78 % 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: 0.58 (0.16), residues: 2559 helix: 0.72 (0.14), residues: 1227 sheet: 0.59 (0.26), residues: 393 loop : 0.05 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 231 HIS 0.009 0.001 HIS B 168 PHE 0.035 0.002 PHE C 248 TYR 0.024 0.002 TYR K 184 ARG 0.009 0.000 ARG G 117 *********************** 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 316 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 250 time to evaluate : 2.659 Fit side-chains TARDY: cannot create tardy model for: "GLN B 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 145 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7166 (tp40) REVERT: C 262 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8706 (mt) REVERT: E 145 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8193 (tt0) REVERT: E 245 LEU cc_start: 0.8822 (mp) cc_final: 0.8525 (tt) REVERT: I 245 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8552 (tt) REVERT: G 154 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8073 (tt0) REVERT: G 223 ASN cc_start: 0.8121 (OUTLIER) cc_final: 0.7914 (t0) REVERT: F 13 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: F 47 ASP cc_start: 0.7383 (m-30) cc_final: 0.7137 (m-30) outliers start: 66 outliers final: 38 residues processed: 295 average time/residue: 1.5702 time to fit residues: 520.6299 Evaluate side-chains 290 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 245 time to evaluate : 2.545 ------------------------------------------------------------------------------- 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 145 GLN Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 263 THR 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 93 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 145 GLN Chi-restraints excluded: chain E residue 292 ARG Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 397 THR 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 245 LEU Chi-restraints excluded: chain I residue 292 ARG Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 93 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 223 optimal weight: 6.9990 chunk 235 optimal weight: 0.9990 chunk 214 optimal weight: 0.0170 chunk 229 optimal weight: 8.9990 chunk 137 optimal weight: 10.0000 chunk 99 optimal weight: 0.0870 chunk 179 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 206 optimal weight: 7.9990 chunk 216 optimal weight: 3.9990 chunk 228 optimal weight: 7.9990 overall best weight: 1.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 GLN I 168 ASN ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23124 Z= 0.204 Angle : 0.607 9.394 31287 Z= 0.312 Chirality : 0.046 0.266 3207 Planarity : 0.005 0.056 3729 Dihedral : 18.845 179.369 4164 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.85 % Favored : 94.92 % Rotamer: Outliers : 2.70 % Allowed : 18.47 % Favored : 78.83 % 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: 0.66 (0.17), residues: 2559 helix: 0.82 (0.15), residues: 1218 sheet: 0.66 (0.26), residues: 393 loop : 0.02 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 206 HIS 0.004 0.001 HIS B 168 PHE 0.036 0.001 PHE C 248 TYR 0.021 0.001 TYR K 184 ARG 0.009 0.000 ARG G 117 *********************** 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 309 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 250 time to evaluate : 2.602 Fit side-chains TARDY: cannot create tardy model for: "GLN B 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 45 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7396 (mtp85) REVERT: A 112 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.7508 (mtt90) REVERT: A 145 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7192 (tp40) REVERT: E 145 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8090 (tt0) REVERT: E 245 LEU cc_start: 0.8816 (mp) cc_final: 0.8521 (tt) REVERT: I 45 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7929 (mtp85) REVERT: I 245 LEU cc_start: 0.8798 (mm) cc_final: 0.8542 (tt) REVERT: G 154 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7928 (tt0) REVERT: G 214 VAL cc_start: 0.8825 (OUTLIER) cc_final: 0.8521 (p) REVERT: G 223 ASN cc_start: 0.7944 (OUTLIER) cc_final: 0.7634 (t0) REVERT: F 13 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8087 (tt0) REVERT: F 47 ASP cc_start: 0.7390 (m-30) cc_final: 0.7134 (m-30) REVERT: F 150 MET cc_start: 0.7905 (tpt) cc_final: 0.7505 (tpt) outliers start: 59 outliers final: 39 residues processed: 295 average time/residue: 1.5939 time to fit residues: 528.7244 Evaluate side-chains 293 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 245 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 45 ARG 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 145 GLN Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 263 THR 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 244 LEU Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 145 GLN Chi-restraints excluded: chain E residue 292 ARG Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 292 ARG Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain F residue 13 GLU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 150 optimal weight: 20.0000 chunk 242 optimal weight: 6.9990 chunk 147 optimal weight: 0.5980 chunk 114 optimal weight: 9.9990 chunk 168 optimal weight: 8.9990 chunk 254 optimal weight: 10.0000 chunk 233 optimal weight: 4.9990 chunk 202 optimal weight: 30.0000 chunk 21 optimal weight: 0.9990 chunk 156 optimal weight: 5.9990 chunk 124 optimal weight: 0.5980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 GLN I 168 ASN ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23124 Z= 0.260 Angle : 0.637 9.439 31287 Z= 0.328 Chirality : 0.048 0.265 3207 Planarity : 0.005 0.058 3729 Dihedral : 18.638 177.764 4163 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.57 % Favored : 95.15 % Rotamer: Outliers : 2.38 % Allowed : 18.79 % Favored : 78.83 % 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: 0.60 (0.16), residues: 2559 helix: 0.78 (0.15), residues: 1218 sheet: 0.60 (0.26), residues: 393 loop : 0.00 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 231 HIS 0.006 0.001 HIS B 168 PHE 0.040 0.002 PHE C 248 TYR 0.022 0.002 TYR K 184 ARG 0.009 0.000 ARG G 117 ********************** 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 300 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 248 time to evaluate : 2.693 Fit side-chains TARDY: cannot create tardy model for: "GLN B 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN F 245 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN J 245 " (corrupted residue). Skipping it. REVERT: A 112 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.7536 (mtt90) REVERT: A 145 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7216 (tp40) REVERT: E 145 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8154 (tt0) REVERT: E 245 LEU cc_start: 0.8813 (mp) cc_final: 0.8515 (tt) REVERT: I 245 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8545 (tt) REVERT: G 154 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8021 (tt0) REVERT: F 47 ASP cc_start: 0.7379 (m-30) cc_final: 0.7111 (m-30) outliers start: 52 outliers final: 41 residues processed: 286 average time/residue: 1.5674 time to fit residues: 504.4863 Evaluate side-chains 291 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 245 time to evaluate : 2.462 ------------------------------------------------------------------------------- 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 145 GLN Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 263 THR 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 93 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 145 GLN Chi-restraints excluded: chain E residue 292 ARG Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 397 THR 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 245 LEU Chi-restraints excluded: chain I residue 292 ARG Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 160 optimal weight: 6.9990 chunk 215 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 186 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 202 optimal weight: 30.0000 chunk 84 optimal weight: 7.9990 chunk 208 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 GLN ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.119793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.088062 restraints weight = 23718.571| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.52 r_work: 0.2873 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23124 Z= 0.276 Angle : 0.643 10.134 31287 Z= 0.332 Chirality : 0.048 0.269 3207 Planarity : 0.005 0.057 3729 Dihedral : 18.578 175.782 4162 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.65 % Favored : 95.08 % Rotamer: Outliers : 2.47 % Allowed : 18.88 % Favored : 78.65 % 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: 0.58 (0.16), residues: 2559 helix: 0.75 (0.15), residues: 1221 sheet: 0.58 (0.26), residues: 393 loop : 0.00 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 231 HIS 0.006 0.001 HIS B 168 PHE 0.041 0.002 PHE C 248 TYR 0.022 0.002 TYR K 184 ARG 0.009 0.000 ARG G 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10791.13 seconds wall clock time: 190 minutes 56.63 seconds (11456.63 seconds total)