Starting phenix.real_space_refine on Sat Feb 24 13:49:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4k_24829/02_2024/7s4k_24829_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4k_24829/02_2024/7s4k_24829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4k_24829/02_2024/7s4k_24829.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4k_24829/02_2024/7s4k_24829.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4k_24829/02_2024/7s4k_24829_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4k_24829/02_2024/7s4k_24829_trim_updated.pdb" } resolution = 2.36 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 19395 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Cu 9 5.60 5 P 36 5.49 5 S 93 5.16 5 C 15030 2.51 5 N 3417 2.21 5 O 4004 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22589 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3017 Classifications: {'peptide': 382} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 356} Chain: "C" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1972 Classifications: {'peptide': 236} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain: "B" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1977 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "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: "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: "F" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1977 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "J" Number of atoms: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1977 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' CU': 2, 'D10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 315 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 284 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "G" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 273 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "K" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 189 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} 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: "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: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 284 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "I" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "F" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "J" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Time building chain proxies: 11.78, per 1000 atoms: 0.52 Number of scatterers: 22589 At special positions: 0 Unit cell: (107.194, 107.667, 118.056, 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 4004 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: 10.07 Conformation dependent library (CDL) restraints added in 4.4 seconds 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4758 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 81 helices and 24 sheets defined 48.0% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.11 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: 3.523A pdb=" N ILE A 379 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 72 removed outlier: 3.962A 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 162 Processing helix chain 'C' and resid 171 through 177 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: 3.636A pdb=" N ILE C 220 " --> pdb=" O GLY C 216 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU C 221 " --> pdb=" O PRO C 217 " (cutoff:3.500A) Proline residue: C 222 - end of helix removed outlier: 4.653A pdb=" N GLY C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU C 226 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 269 removed outlier: 4.372A pdb=" N GLY C 247 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 44 Processing helix chain 'B' and resid 46 through 50 Processing helix chain 'B' and resid 59 through 83 Proline residue: B 65 - end of helix removed outlier: 4.442A pdb=" N THR B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N PHE B 71 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Proline residue: B 72 - end of helix removed outlier: 3.867A 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: 4.213A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE B 156 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N TYR B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Proline residue: B 158 - end of helix Proline residue: B 162 - end of helix Proline residue: B 166 - end of helix Processing helix chain 'B' and resid 180 through 187 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 212 through 238 removed outlier: 3.789A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 72 removed outlier: 3.963A 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 162 Processing helix chain 'G' and resid 171 through 177 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: 3.636A pdb=" N ILE G 220 " --> pdb=" O GLY G 216 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU G 221 " --> pdb=" O PRO G 217 " (cutoff:3.500A) Proline residue: G 222 - end of helix removed outlier: 4.653A pdb=" N GLY G 225 " --> pdb=" O LEU G 221 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU G 226 " --> pdb=" O PRO G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 269 removed outlier: 4.372A pdb=" N GLY G 247 " --> pdb=" O LEU G 244 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 72 removed outlier: 3.963A 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 162 Processing helix chain 'K' and resid 171 through 177 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: 3.636A pdb=" N ILE K 220 " --> pdb=" O GLY K 216 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU K 221 " --> pdb=" O PRO K 217 " (cutoff:3.500A) Proline residue: K 222 - end of helix removed outlier: 4.653A pdb=" N GLY K 225 " --> pdb=" O LEU K 221 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU K 226 " --> pdb=" O PRO K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 243 through 269 removed outlier: 4.371A pdb=" N GLY K 247 " --> pdb=" O LEU K 244 " (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: 3.522A pdb=" N ILE E 379 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 3.658A 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: 3.523A pdb=" N ILE I 379 " --> pdb=" O LEU I 376 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE I 380 " --> pdb=" O SER I 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 44 Processing helix chain 'F' and resid 46 through 50 Processing helix chain 'F' and resid 59 through 83 Proline residue: F 65 - end of helix removed outlier: 4.442A pdb=" N THR F 70 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N PHE F 71 " --> pdb=" O VAL F 67 " (cutoff:3.500A) Proline residue: F 72 - end of helix removed outlier: 3.868A 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: 4.213A pdb=" N ALA F 149 " --> pdb=" O ALA F 145 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE F 156 " --> pdb=" O TRP F 152 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N TYR F 157 " --> pdb=" O GLY F 153 " (cutoff:3.500A) Proline residue: F 158 - end of helix Proline residue: F 162 - end of helix Proline residue: F 166 - end of helix Processing helix chain 'F' and resid 180 through 187 Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 212 through 238 removed outlier: 3.789A pdb=" N PHE F 233 " --> pdb=" O PHE F 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 44 Processing helix chain 'J' and resid 46 through 50 Processing helix chain 'J' and resid 59 through 83 Proline residue: J 65 - end of helix removed outlier: 4.443A pdb=" N THR J 70 " --> pdb=" O ILE J 66 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N PHE J 71 " --> pdb=" O VAL J 67 " (cutoff:3.500A) Proline residue: J 72 - end of helix removed outlier: 3.867A 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: 4.212A pdb=" N ALA J 149 " --> pdb=" O ALA J 145 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE J 156 " --> pdb=" O TRP J 152 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N TYR J 157 " --> pdb=" O GLY J 153 " (cutoff:3.500A) Proline residue: J 158 - end of helix Proline residue: J 162 - end of helix Proline residue: J 166 - end of helix Processing helix chain 'J' and resid 180 through 187 Processing helix chain 'J' and resid 195 through 197 No H-bonds generated for 'chain 'J' and resid 195 through 197' Processing helix chain 'J' and resid 212 through 238 removed outlier: 3.788A pdb=" N PHE J 233 " --> pdb=" O PHE J 229 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 47 through 50 removed outlier: 6.723A pdb=" N LYS A 129 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 5.813A 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: 8.342A pdb=" N VAL A 59 " --> pdb=" O TRP A 156 " (cutoff:3.500A) removed outlier: 6.202A 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: 6.536A 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: 6.668A pdb=" N PHE A 392 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE A 317 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 6.383A 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: 6.722A pdb=" N LYS E 129 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 5.813A 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: 8.342A pdb=" N VAL E 59 " --> pdb=" O TRP E 156 " (cutoff:3.500A) removed outlier: 6.202A 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: 6.537A 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: 6.668A pdb=" N PHE E 392 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE E 317 " --> pdb=" O LEU E 390 " (cutoff:3.500A) removed outlier: 6.384A 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: 6.723A pdb=" N LYS I 129 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 5.812A 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: 8.342A pdb=" N VAL I 59 " --> pdb=" O TRP I 156 " (cutoff:3.500A) removed outlier: 6.202A 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: 6.536A 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: 6.668A pdb=" N PHE I 392 " --> pdb=" O GLY I 315 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE I 317 " --> pdb=" O LEU I 390 " (cutoff:3.500A) removed outlier: 6.383A 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 1023 hydrogen bonds defined for protein. 2808 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: 6.64 Time building geometry restraints manager: 10.71 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: 3292 1.32 - 1.44: 6810 1.44 - 1.56: 12679 1.56 - 1.69: 166 1.69 - 1.81: 180 Bond restraints: 23127 Sorted by residual: 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 4.05e+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 4.04e+01 bond pdb=" CB PLC G 301 " pdb=" O3 PLC G 301 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" CB PLC B 301 " pdb=" O3 PLC B 301 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" CB PLC F 302 " pdb=" O3 PLC F 302 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 4.00e+01 ... (remaining 23122 not shown) Histogram of bond angle deviations from ideal: 99.62 - 107.36: 1087 107.36 - 115.09: 13537 115.09 - 122.83: 14613 122.83 - 130.56: 1888 130.56 - 138.30: 168 Bond angle restraints: 31293 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 112.96 134.60 -21.64 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 305 " pdb=" CA' PLC J 305 " pdb=" CB' PLC J 305 " ideal model delta sigma weight residual 112.96 134.53 -21.57 3.00e+00 1.11e-01 5.17e+01 angle pdb=" CA HIS G 173 " pdb=" CB HIS G 173 " pdb=" CG HIS G 173 " ideal model delta sigma weight residual 113.80 120.87 -7.07 1.00e+00 1.00e+00 5.00e+01 angle pdb=" CA HIS K 173 " pdb=" CB HIS K 173 " pdb=" CG HIS K 173 " ideal model delta sigma weight residual 113.80 120.85 -7.05 1.00e+00 1.00e+00 4.97e+01 ... (remaining 31288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.45: 12596 34.45 - 68.90: 823 68.90 - 103.35: 72 103.35 - 137.80: 33 137.80 - 172.25: 21 Dihedral angle restraints: 13545 sinusoidal: 6093 harmonic: 7452 Sorted by residual: dihedral pdb=" CA GLN C 276 " pdb=" C GLN C 276 " pdb=" N SER C 277 " pdb=" CA SER C 277 " ideal model delta harmonic sigma weight residual -180.00 -155.36 -24.64 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA GLN G 276 " pdb=" C GLN G 276 " pdb=" N SER G 277 " pdb=" CA SER G 277 " ideal model delta harmonic sigma weight residual -180.00 -155.38 -24.62 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA GLN K 276 " pdb=" C GLN K 276 " pdb=" N SER K 277 " pdb=" CA SER K 277 " ideal model delta harmonic sigma weight residual -180.00 -155.39 -24.61 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 13542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2340 0.048 - 0.096: 613 0.096 - 0.145: 199 0.145 - 0.193: 32 0.193 - 0.241: 23 Chirality restraints: 3207 Sorted by residual: chirality pdb=" C2 PLC K 305 " pdb=" C1 PLC K 305 " pdb=" C3 PLC K 305 " pdb=" O2 PLC K 305 " both_signs ideal model delta sigma weight residual False -2.31 -2.55 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C2 PLC G 307 " pdb=" C1 PLC G 307 " pdb=" C3 PLC G 307 " pdb=" O2 PLC G 307 " both_signs ideal model delta sigma weight residual False -2.31 -2.55 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C2 PLC C 307 " pdb=" C1 PLC C 307 " pdb=" C3 PLC C 307 " pdb=" O2 PLC C 307 " both_signs ideal model delta sigma weight residual False -2.31 -2.55 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 3204 not shown) Planarity restraints: 3732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS G 160 " 0.030 2.00e-02 2.50e+03 2.70e-02 1.09e+01 pdb=" CG HIS G 160 " -0.055 2.00e-02 2.50e+03 pdb=" ND1 HIS G 160 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS G 160 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS G 160 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS G 160 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 160 " -0.029 2.00e-02 2.50e+03 2.69e-02 1.09e+01 pdb=" CG HIS C 160 " 0.055 2.00e-02 2.50e+03 pdb=" ND1 HIS C 160 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS C 160 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS C 160 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS C 160 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS K 160 " 0.029 2.00e-02 2.50e+03 2.68e-02 1.08e+01 pdb=" CG HIS K 160 " -0.055 2.00e-02 2.50e+03 pdb=" ND1 HIS K 160 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS K 160 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS K 160 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS K 160 " 0.021 2.00e-02 2.50e+03 ... (remaining 3729 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 21 2.14 - 2.83: 7106 2.83 - 3.52: 32076 3.52 - 4.21: 62137 4.21 - 4.90: 105761 Nonbonded interactions: 207101 Sorted by model distance: nonbonded pdb=" NE2 HIS K 245 " pdb="CU CU K 301 " model vdw 1.448 2.320 nonbonded pdb=" NE2 HIS G 245 " pdb="CU CU G 302 " model vdw 1.448 2.320 nonbonded pdb=" NE2 HIS C 245 " pdb="CU CU C 301 " model vdw 1.448 2.320 nonbonded pdb=" ND1 HIS E 48 " pdb="CU CU E 502 " model vdw 1.975 2.320 nonbonded pdb=" ND1 HIS A 48 " pdb="CU CU A 502 " model vdw 1.976 2.320 ... (remaining 207096 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) selection = (chain 'F' and resid 7 through 247) selection = (chain 'J' and resid 7 through 247) } ncs_group { reference = (chain 'C' and (resid 45 through 280 or resid 305)) selection = (chain 'G' and (resid 45 through 280 or resid 305)) selection = (chain 'K' and (resid 45 through 280 or resid 305)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.240 Construct map_model_manager: 0.010 Extract box with map and model: 17.830 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 61.510 Find NCS groups from input model: 1.570 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:11.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.127 23127 Z= 0.551 Angle : 1.049 21.643 31293 Z= 0.524 Chirality : 0.052 0.241 3207 Planarity : 0.005 0.041 3732 Dihedral : 22.366 172.246 8787 Min Nonbonded Distance : 1.448 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.39 % Favored : 94.37 % Rotamer: Outliers : 3.29 % Allowed : 18.24 % Favored : 78.46 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.17), residues: 2559 helix: 1.03 (0.15), residues: 1185 sheet: 1.09 (0.31), residues: 333 loop : -0.29 (0.20), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 206 HIS 0.024 0.003 HIS I 33 PHE 0.017 0.002 PHE J 31 TYR 0.021 0.001 TYR G 184 ARG 0.008 0.001 ARG K 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 228 time to evaluate : 2.400 Fit side-chains revert: symmetry clash REVERT: C 48 LYS cc_start: 0.7424 (ptmt) cc_final: 0.7139 (ptmm) REVERT: K 48 LYS cc_start: 0.7482 (ptmt) cc_final: 0.7238 (ptmm) REVERT: K 49 LYS cc_start: 0.6161 (pptt) cc_final: 0.5793 (pmtt) REVERT: K 117 ARG cc_start: 0.8516 (mmt-90) cc_final: 0.8247 (mmt90) REVERT: E 163 MET cc_start: 0.8938 (ttt) cc_final: 0.8709 (ttt) REVERT: I 163 MET cc_start: 0.8980 (ttt) cc_final: 0.8680 (ttt) REVERT: F 49 ASP cc_start: 0.8774 (t70) cc_final: 0.8474 (t70) REVERT: F 172 GLU cc_start: 0.8308 (tm-30) cc_final: 0.8069 (tm-30) outliers start: 72 outliers final: 40 residues processed: 286 average time/residue: 1.5221 time to fit residues: 490.1674 Evaluate side-chains 255 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 215 time to evaluate : 2.524 ------------------------------------------------------------------------------- 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 180 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 378 ASP Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 180 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 215 optimal weight: 0.9980 chunk 193 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 199 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 148 optimal weight: 6.9990 chunk 231 optimal weight: 9.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN G 118 ASN G 161 GLN K 161 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23127 Z= 0.269 Angle : 0.608 5.978 31293 Z= 0.311 Chirality : 0.047 0.329 3207 Planarity : 0.005 0.043 3732 Dihedral : 22.598 179.037 4221 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.14 % Favored : 95.51 % Rotamer: Outliers : 3.34 % Allowed : 17.56 % Favored : 79.10 % 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: 0.80 (0.17), residues: 2559 helix: 1.11 (0.15), residues: 1206 sheet: 1.00 (0.29), residues: 342 loop : -0.23 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 231 HIS 0.005 0.001 HIS C 160 PHE 0.022 0.002 PHE C 248 TYR 0.020 0.002 TYR C 184 ARG 0.007 0.000 ARG B 206 *********************** 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 302 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 229 time to evaluate : 2.556 Fit side-chains REVERT: A 112 ARG cc_start: 0.9229 (OUTLIER) cc_final: 0.8527 (mtt90) REVERT: A 404 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8346 (tt0) REVERT: C 48 LYS cc_start: 0.7462 (ptmt) cc_final: 0.7173 (ptmm) REVERT: G 48 LYS cc_start: 0.7553 (ptmt) cc_final: 0.7237 (ptmm) REVERT: K 48 LYS cc_start: 0.7533 (ptmt) cc_final: 0.7212 (ptmm) REVERT: K 117 ARG cc_start: 0.8443 (mmt-90) cc_final: 0.8212 (mmt90) REVERT: E 112 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8051 (mtt90) REVERT: E 163 MET cc_start: 0.8998 (ttt) cc_final: 0.8783 (ttt) REVERT: I 163 MET cc_start: 0.9025 (ttt) cc_final: 0.8776 (ttt) REVERT: F 172 GLU cc_start: 0.8280 (tm-30) cc_final: 0.8004 (tm-30) REVERT: J 16 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8063 (tt0) outliers start: 73 outliers final: 35 residues processed: 282 average time/residue: 1.5412 time to fit residues: 489.4441 Evaluate side-chains 257 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 218 time to evaluate : 2.574 ------------------------------------------------------------------------------- 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 309 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 279 CYS Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 234 TRP Chi-restraints excluded: chain K residue 279 CYS Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain J residue 16 GLN Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 180 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 128 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 192 optimal weight: 10.0000 chunk 157 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 chunk 250 optimal weight: 6.9990 chunk 206 optimal weight: 4.9990 chunk 230 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 186 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 GLN C 161 GLN G 161 GLN K 161 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 23127 Z= 0.309 Angle : 0.603 6.023 31293 Z= 0.313 Chirality : 0.047 0.243 3207 Planarity : 0.005 0.045 3732 Dihedral : 21.487 177.702 4189 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.18 % Favored : 95.55 % Rotamer: Outliers : 3.29 % Allowed : 17.33 % Favored : 79.38 % 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: 0.73 (0.17), residues: 2559 helix: 1.05 (0.15), residues: 1215 sheet: 0.91 (0.27), residues: 372 loop : -0.30 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 152 HIS 0.006 0.001 HIS K 160 PHE 0.020 0.002 PHE K 251 TYR 0.022 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 291 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 219 time to evaluate : 2.519 Fit side-chains REVERT: A 112 ARG cc_start: 0.9300 (OUTLIER) cc_final: 0.7851 (mtt90) REVERT: A 404 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8367 (tt0) REVERT: C 48 LYS cc_start: 0.7400 (ptmt) cc_final: 0.7127 (ptmm) REVERT: G 48 LYS cc_start: 0.7366 (ptmt) cc_final: 0.7117 (ptmm) REVERT: K 48 LYS cc_start: 0.7454 (ptmt) cc_final: 0.7199 (ptmm) REVERT: E 112 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.7975 (mtt90) REVERT: I 112 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.7827 (mtt90) REVERT: F 172 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7965 (tm-30) outliers start: 72 outliers final: 39 residues processed: 272 average time/residue: 1.5739 time to fit residues: 483.0126 Evaluate side-chains 253 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 210 time to evaluate : 2.405 ------------------------------------------------------------------------------- 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 309 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 279 CYS 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 G residue 74 TRP Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 279 CYS Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 279 CYS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 180 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 229 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 232 optimal weight: 0.9990 chunk 246 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 220 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 GLN C 161 GLN G 161 GLN K 161 GLN ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 23127 Z= 0.365 Angle : 0.625 7.195 31293 Z= 0.324 Chirality : 0.048 0.272 3207 Planarity : 0.005 0.046 3732 Dihedral : 21.039 179.635 4188 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.99 % Favored : 95.66 % Rotamer: Outliers : 3.43 % Allowed : 17.47 % Favored : 79.10 % 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: 0.67 (0.17), residues: 2559 helix: 0.98 (0.15), residues: 1215 sheet: 0.83 (0.27), residues: 372 loop : -0.26 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 231 HIS 0.004 0.001 HIS K 160 PHE 0.020 0.002 PHE C 248 TYR 0.022 0.002 TYR K 184 ARG 0.010 0.000 ARG J 206 *********************** 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 294 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 219 time to evaluate : 2.264 Fit side-chains REVERT: A 112 ARG cc_start: 0.9320 (OUTLIER) cc_final: 0.7878 (mtt90) REVERT: C 46 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7683 (mp) REVERT: C 48 LYS cc_start: 0.7386 (ptmt) cc_final: 0.7121 (ptmm) REVERT: B 172 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7883 (tm-30) REVERT: G 48 LYS cc_start: 0.7374 (ptmt) cc_final: 0.7135 (ptmm) REVERT: K 46 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7703 (mp) REVERT: K 48 LYS cc_start: 0.7391 (ptmt) cc_final: 0.7152 (ptmm) REVERT: K 117 ARG cc_start: 0.8485 (mmt-90) cc_final: 0.8219 (mmt90) REVERT: E 112 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8241 (mtt90) REVERT: E 404 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8116 (tt0) REVERT: I 112 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.7830 (mtt90) REVERT: F 172 GLU cc_start: 0.8327 (tm-30) cc_final: 0.7999 (tm-30) outliers start: 75 outliers final: 45 residues processed: 274 average time/residue: 1.5707 time to fit residues: 484.1495 Evaluate side-chains 264 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 213 time to evaluate : 2.444 ------------------------------------------------------------------------------- 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 108 GLN Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 279 CYS 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 G residue 74 TRP Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 279 CYS Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 279 CYS Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 108 GLN Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 176 GLN Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 208 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 230 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 205 optimal weight: 0.9980 chunk 139 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 183 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 221 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN G 161 GLN K 161 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 23127 Z= 0.322 Angle : 0.602 6.693 31293 Z= 0.312 Chirality : 0.047 0.253 3207 Planarity : 0.005 0.046 3732 Dihedral : 20.603 176.201 4184 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.06 % Favored : 95.62 % Rotamer: Outliers : 3.66 % Allowed : 17.33 % 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: 0.72 (0.17), residues: 2559 helix: 1.01 (0.15), residues: 1215 sheet: 0.84 (0.27), residues: 372 loop : -0.21 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 231 HIS 0.003 0.001 HIS A 139 PHE 0.019 0.002 PHE K 248 TYR 0.021 0.002 TYR K 184 ARG 0.009 0.000 ARG C 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 299 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 219 time to evaluate : 2.516 Fit side-chains REVERT: A 112 ARG cc_start: 0.9317 (OUTLIER) cc_final: 0.7918 (mtt90) REVERT: C 46 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7652 (mp) REVERT: C 48 LYS cc_start: 0.7331 (ptmt) cc_final: 0.7088 (ptmm) REVERT: B 172 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7881 (tm-30) REVERT: G 48 LYS cc_start: 0.7334 (ptmt) cc_final: 0.7115 (ptmm) REVERT: K 48 LYS cc_start: 0.7325 (ptmt) cc_final: 0.7106 (ptmm) REVERT: K 117 ARG cc_start: 0.8466 (mmt-90) cc_final: 0.8225 (mmt90) REVERT: E 112 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.8250 (mtt90) REVERT: E 404 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8240 (tt0) REVERT: I 45 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.7340 (mtp85) REVERT: I 112 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.7827 (mtt90) REVERT: I 404 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8366 (tt0) REVERT: F 172 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7963 (tm-30) outliers start: 80 outliers final: 48 residues processed: 277 average time/residue: 1.5255 time to fit residues: 476.6338 Evaluate side-chains 268 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 213 time to evaluate : 2.364 ------------------------------------------------------------------------------- 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 108 GLN Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 279 CYS 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 G residue 74 TRP Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 279 CYS Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 167 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 208 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 176 GLN Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 208 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 404 GLN Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 135 LEU 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: 5.9990 chunk 221 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 144 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 246 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 129 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN G 161 GLN K 161 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23127 Z= 0.248 Angle : 0.572 6.685 31293 Z= 0.296 Chirality : 0.046 0.237 3207 Planarity : 0.004 0.045 3732 Dihedral : 20.179 172.704 4183 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.45 % Favored : 95.35 % Rotamer: Outliers : 3.38 % Allowed : 17.74 % Favored : 78.88 % 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: 0.81 (0.17), residues: 2559 helix: 1.08 (0.15), residues: 1215 sheet: 0.89 (0.27), residues: 372 loop : -0.17 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 231 HIS 0.003 0.001 HIS I 139 PHE 0.019 0.001 PHE K 248 TYR 0.021 0.001 TYR G 184 ARG 0.010 0.000 ARG C 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 292 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 218 time to evaluate : 2.478 Fit side-chains REVERT: A 45 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.6851 (mtp85) REVERT: A 112 ARG cc_start: 0.9299 (OUTLIER) cc_final: 0.7931 (mtt90) REVERT: C 46 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7649 (mp) REVERT: C 48 LYS cc_start: 0.7343 (ptmt) cc_final: 0.7110 (ptmm) REVERT: B 172 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7816 (tm-30) REVERT: G 48 LYS cc_start: 0.7285 (ptmt) cc_final: 0.7079 (ptmm) REVERT: K 48 LYS cc_start: 0.7258 (ptmt) cc_final: 0.7046 (ptmm) REVERT: K 117 ARG cc_start: 0.8438 (mmt-90) cc_final: 0.8228 (mmt90) REVERT: E 112 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8087 (mtt90) REVERT: E 363 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.8062 (t70) REVERT: I 45 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7298 (mtp85) REVERT: I 112 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.7864 (mtt90) REVERT: I 123 ASP cc_start: 0.8192 (p0) cc_final: 0.7856 (p0) REVERT: F 172 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7930 (tm-30) outliers start: 74 outliers final: 41 residues processed: 271 average time/residue: 1.5709 time to fit residues: 478.6934 Evaluate side-chains 260 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 212 time to evaluate : 2.730 ------------------------------------------------------------------------------- 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 108 GLN Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 80 SER Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 363 ASP Chi-restraints excluded: chain E residue 397 THR 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 112 ARG Chi-restraints excluded: chain I residue 176 GLN Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 208 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain F residue 8 VAL 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 J residue 8 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 135 LEU 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: 7.9990 chunk 27 optimal weight: 0.8980 chunk 140 optimal weight: 0.0170 chunk 180 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 245 optimal weight: 6.9990 chunk 153 optimal weight: 0.0040 chunk 149 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.9632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN G 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23127 Z= 0.162 Angle : 0.535 6.477 31293 Z= 0.274 Chirality : 0.044 0.207 3207 Planarity : 0.004 0.043 3732 Dihedral : 19.433 168.445 4180 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.61 % Favored : 95.23 % Rotamer: Outliers : 2.38 % Allowed : 18.66 % Favored : 78.97 % 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: 0.97 (0.17), residues: 2559 helix: 1.27 (0.15), residues: 1206 sheet: 0.82 (0.27), residues: 387 loop : -0.10 (0.21), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 202 HIS 0.002 0.001 HIS A 139 PHE 0.017 0.001 PHE K 248 TYR 0.021 0.001 TYR G 184 ARG 0.010 0.000 ARG C 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 287 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 235 time to evaluate : 2.520 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.6679 (mtp85) REVERT: A 112 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.8082 (mtt90) REVERT: C 46 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7574 (mp) REVERT: C 48 LYS cc_start: 0.7276 (ptmt) cc_final: 0.7051 (ptmm) REVERT: B 172 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7755 (tm-30) REVERT: B 206 ARG cc_start: 0.7966 (mmm-85) cc_final: 0.7730 (mtp85) REVERT: G 237 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.6512 (mp0) REVERT: E 112 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.7974 (mtt90) REVERT: I 45 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.6995 (mtp85) REVERT: I 112 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.7903 (mtt90) REVERT: I 123 ASP cc_start: 0.8097 (p0) cc_final: 0.7772 (p0) REVERT: F 172 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7885 (tm-30) outliers start: 52 outliers final: 34 residues processed: 273 average time/residue: 1.6070 time to fit residues: 492.8454 Evaluate side-chains 264 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 223 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain B residue 8 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 G residue 74 TRP Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 237 GLU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 397 THR 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 112 ARG Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU 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: 1.9990 chunk 98 optimal weight: 0.8980 chunk 146 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 156 optimal weight: 9.9990 chunk 167 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 22 optimal weight: 0.0020 chunk 193 optimal weight: 4.9990 overall best weight: 1.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 161 GLN I 108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23127 Z= 0.194 Angle : 0.549 8.226 31293 Z= 0.281 Chirality : 0.044 0.208 3207 Planarity : 0.004 0.044 3732 Dihedral : 19.059 167.251 4179 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.45 % Favored : 95.39 % Rotamer: Outliers : 2.70 % Allowed : 18.24 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.17), residues: 2559 helix: 1.28 (0.15), residues: 1200 sheet: 0.81 (0.27), residues: 390 loop : -0.06 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 152 HIS 0.003 0.001 HIS I 139 PHE 0.026 0.001 PHE C 248 TYR 0.021 0.001 TYR G 184 ARG 0.009 0.000 ARG C 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 285 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 226 time to evaluate : 2.496 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.6752 (mtp85) REVERT: A 112 ARG cc_start: 0.9262 (OUTLIER) cc_final: 0.8021 (mtt90) REVERT: C 46 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7598 (mp) REVERT: C 48 LYS cc_start: 0.7288 (ptmt) cc_final: 0.7077 (ptmm) REVERT: B 172 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7745 (tm-30) REVERT: B 206 ARG cc_start: 0.7973 (mmm-85) cc_final: 0.7743 (mtp85) REVERT: G 237 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.6449 (mp0) REVERT: E 112 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.7972 (mtt90) REVERT: E 404 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7750 (tt0) REVERT: I 45 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7169 (mtp85) REVERT: I 112 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.7835 (mtt90) REVERT: I 123 ASP cc_start: 0.8106 (p0) cc_final: 0.7786 (p0) REVERT: F 172 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7868 (tm-30) outliers start: 59 outliers final: 38 residues processed: 269 average time/residue: 1.5998 time to fit residues: 482.9716 Evaluate side-chains 270 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 224 time to evaluate : 2.699 ------------------------------------------------------------------------------- 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 309 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain B residue 8 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 G residue 74 TRP Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 237 GLU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 404 GLN 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 108 GLN Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 241 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 223 optimal weight: 0.0980 chunk 235 optimal weight: 5.9990 chunk 214 optimal weight: 1.9990 chunk 229 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 179 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 206 optimal weight: 7.9990 chunk 216 optimal weight: 6.9990 chunk 228 optimal weight: 5.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23127 Z= 0.278 Angle : 0.585 8.831 31293 Z= 0.302 Chirality : 0.046 0.222 3207 Planarity : 0.004 0.045 3732 Dihedral : 18.938 167.024 4179 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.30 % Favored : 95.55 % Rotamer: Outliers : 2.61 % Allowed : 18.47 % Favored : 78.92 % 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: 0.95 (0.17), residues: 2559 helix: 1.19 (0.15), residues: 1203 sheet: 0.96 (0.27), residues: 372 loop : -0.08 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 152 HIS 0.003 0.001 HIS I 139 PHE 0.026 0.002 PHE C 248 TYR 0.022 0.002 TYR C 184 ARG 0.010 0.000 ARG K 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 281 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 224 time to evaluate : 2.371 Fit side-chains REVERT: A 45 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.6846 (mtp85) REVERT: A 112 ARG cc_start: 0.9292 (OUTLIER) cc_final: 0.7946 (mtt90) REVERT: A 287 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7581 (mm-30) REVERT: C 46 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7655 (mp) REVERT: C 48 LYS cc_start: 0.7343 (ptmt) cc_final: 0.7114 (ptmm) REVERT: B 172 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7804 (tm-30) REVERT: B 206 ARG cc_start: 0.8039 (mmm-85) cc_final: 0.7824 (mtp85) REVERT: G 237 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6544 (mp0) REVERT: K 117 ARG cc_start: 0.8503 (mmt-90) cc_final: 0.8209 (mmt90) REVERT: E 112 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.7994 (mtt90) REVERT: E 363 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.8059 (t70) REVERT: E 404 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8029 (tt0) REVERT: I 45 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.7272 (mtp85) REVERT: I 112 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.7840 (mtt90) REVERT: I 123 ASP cc_start: 0.8181 (p0) cc_final: 0.7852 (p0) REVERT: J 198 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.7155 (ttp80) outliers start: 57 outliers final: 37 residues processed: 265 average time/residue: 1.7755 time to fit residues: 532.0764 Evaluate side-chains 268 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 220 time to evaluate : 2.498 ------------------------------------------------------------------------------- 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 287 GLU Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain B residue 8 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 G residue 74 TRP Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 237 GLU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 363 ASP Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 404 GLN 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 112 ARG Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 198 ARG Chi-restraints excluded: chain J residue 241 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 150 optimal weight: 8.9990 chunk 242 optimal weight: 0.7980 chunk 147 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 168 optimal weight: 7.9990 chunk 254 optimal weight: 8.9990 chunk 233 optimal weight: 6.9990 chunk 202 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 276 GLN I 108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23127 Z= 0.193 Angle : 0.554 9.449 31293 Z= 0.284 Chirality : 0.045 0.208 3207 Planarity : 0.004 0.043 3732 Dihedral : 18.506 164.437 4179 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.57 % Favored : 95.27 % Rotamer: Outliers : 2.29 % Allowed : 18.70 % 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: 1.03 (0.17), residues: 2559 helix: 1.25 (0.15), residues: 1203 sheet: 1.02 (0.27), residues: 372 loop : -0.04 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 231 HIS 0.003 0.001 HIS A 139 PHE 0.025 0.001 PHE C 248 TYR 0.021 0.001 TYR G 184 ARG 0.010 0.000 ARG C 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 273 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 223 time to evaluate : 2.473 Fit side-chains REVERT: A 45 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.6714 (mtp85) REVERT: A 112 ARG cc_start: 0.9266 (OUTLIER) cc_final: 0.8016 (mtt90) REVERT: C 46 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7602 (mp) REVERT: C 48 LYS cc_start: 0.7298 (ptmt) cc_final: 0.7091 (ptmm) REVERT: B 172 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7777 (tm-30) REVERT: G 237 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6557 (mp0) REVERT: K 117 ARG cc_start: 0.8480 (mmt-90) cc_final: 0.8194 (mmt90) REVERT: E 112 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.7978 (mtt90) REVERT: E 404 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8196 (tt0) REVERT: I 45 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7194 (mtp85) REVERT: I 112 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.7820 (mtt90) REVERT: I 123 ASP cc_start: 0.8131 (p0) cc_final: 0.7803 (p0) REVERT: F 172 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7821 (tm-30) REVERT: J 198 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.7513 (ttp80) outliers start: 50 outliers final: 38 residues processed: 257 average time/residue: 1.6626 time to fit residues: 477.3825 Evaluate side-chains 269 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 222 time to evaluate : 2.406 ------------------------------------------------------------------------------- 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 309 ASN Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain B residue 8 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 G residue 74 TRP Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 237 GLU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 404 GLN 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 108 GLN Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 359 THR Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain F residue 8 VAL 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 135 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 198 ARG Chi-restraints excluded: chain J residue 241 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 160 optimal weight: 9.9990 chunk 215 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 186 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 202 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 208 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 276 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.104675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.079277 restraints weight = 27994.102| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.73 r_work: 0.2717 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.194 23127 Z= 0.298 Angle : 0.717 59.199 31293 Z= 0.395 Chirality : 0.049 0.982 3207 Planarity : 0.004 0.043 3732 Dihedral : 18.509 164.489 4179 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.61 % Favored : 95.23 % Rotamer: Outliers : 2.19 % Allowed : 18.79 % Favored : 79.01 % 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: 1.02 (0.17), residues: 2559 helix: 1.24 (0.15), residues: 1203 sheet: 1.02 (0.27), residues: 372 loop : -0.04 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 231 HIS 0.003 0.001 HIS I 139 PHE 0.025 0.001 PHE C 248 TYR 0.021 0.001 TYR G 184 ARG 0.008 0.000 ARG C 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8756.29 seconds wall clock time: 157 minutes 13.44 seconds (9433.44 seconds total)