Starting phenix.real_space_refine on Sat Feb 24 14:51:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4i_24827/02_2024/7s4i_24827_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4i_24827/02_2024/7s4i_24827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4i_24827/02_2024/7s4i_24827.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4i_24827/02_2024/7s4i_24827.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4i_24827/02_2024/7s4i_24827_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s4i_24827/02_2024/7s4i_24827_trim_updated.pdb" } resolution = 2.26 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 4249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22834 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: 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: "G" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 315 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "K" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 315 Unusual residues: {' CU': 1, 'D10': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "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: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 200 Unusual residues: {'D10': 4, 'P1O': 2, 'PLC': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "K" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "I" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Chain: "F" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "J" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Time building chain proxies: 11.73, per 1000 atoms: 0.51 Number of scatterers: 22834 At special positions: 0 Unit cell: (106.722, 107.194, 119, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cu 9 28.99 S 93 16.00 P 36 15.00 O 4249 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: 10.70 Conformation dependent library (CDL) restraints added in 3.5 seconds 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4758 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 81 helices and 24 sheets defined 47.5% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.40 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 377 through 381 removed outlier: 3.629A pdb=" N ILE A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 72 removed outlier: 3.906A 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 160 Processing helix chain 'C' and resid 171 through 176 Processing helix chain 'C' and resid 180 through 198 Processing helix chain 'C' and resid 208 through 232 Proline residue: C 217 - end of helix removed outlier: 3.578A pdb=" N ILE C 220 " --> pdb=" O GLY C 216 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU C 221 " --> pdb=" O PRO C 217 " (cutoff:3.500A) Proline residue: C 222 - end of helix removed outlier: 4.662A pdb=" N GLY C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU C 226 " --> pdb=" O PRO C 222 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N HIS C 231 " --> pdb=" O ASN C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 269 removed outlier: 4.420A pdb=" N GLY C 247 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C 250 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE C 251 " --> pdb=" O PHE C 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 44 Processing helix chain 'B' and resid 46 through 50 Processing helix chain 'B' and resid 59 through 83 Proline residue: B 65 - end of helix removed outlier: 4.440A pdb=" N THR B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N PHE B 71 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Proline residue: B 72 - end of helix removed outlier: 3.958A 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: 4.109A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE B 156 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 5.064A 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: 3.765A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 72 removed outlier: 3.906A 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 160 Processing helix chain 'G' and resid 171 through 176 Processing helix chain 'G' and resid 180 through 198 Processing helix chain 'G' and resid 208 through 232 Proline residue: G 217 - end of helix removed outlier: 3.578A pdb=" N ILE G 220 " --> pdb=" O GLY G 216 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU G 221 " --> pdb=" O PRO G 217 " (cutoff:3.500A) Proline residue: G 222 - end of helix removed outlier: 4.662A pdb=" N GLY G 225 " --> pdb=" O LEU G 221 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU G 226 " --> pdb=" O PRO G 222 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N HIS G 231 " --> pdb=" O ASN G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 269 removed outlier: 4.419A pdb=" N GLY G 247 " --> pdb=" O LEU G 244 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE G 250 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE G 251 " --> pdb=" O PHE G 248 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 72 removed outlier: 3.906A 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 160 Processing helix chain 'K' and resid 171 through 176 Processing helix chain 'K' and resid 180 through 198 Processing helix chain 'K' and resid 208 through 232 Proline residue: K 217 - end of helix removed outlier: 3.579A pdb=" N ILE K 220 " --> pdb=" O GLY K 216 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU K 221 " --> pdb=" O PRO K 217 " (cutoff:3.500A) Proline residue: K 222 - end of helix removed outlier: 4.663A pdb=" N GLY K 225 " --> pdb=" O LEU K 221 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU K 226 " --> pdb=" O PRO K 222 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N HIS K 231 " --> pdb=" O ASN K 227 " (cutoff:3.500A) Processing helix chain 'K' and resid 243 through 269 removed outlier: 4.420A pdb=" N GLY K 247 " --> pdb=" O LEU K 244 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE K 250 " --> pdb=" O GLY K 247 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE K 251 " --> pdb=" O PHE K 248 " (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 377 through 381 removed outlier: 3.629A 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 377 through 381 removed outlier: 3.629A 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: 4.440A pdb=" N THR F 70 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N PHE F 71 " --> pdb=" O VAL F 67 " (cutoff:3.500A) Proline residue: F 72 - end of helix removed outlier: 3.959A 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: 4.110A pdb=" N ALA F 149 " --> pdb=" O ALA F 145 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE F 156 " --> pdb=" O TRP F 152 " (cutoff:3.500A) removed outlier: 5.064A 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: 3.765A 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: 4.441A pdb=" N THR J 70 " --> pdb=" O ILE J 66 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N PHE J 71 " --> pdb=" O VAL J 67 " (cutoff:3.500A) Proline residue: J 72 - end of helix removed outlier: 3.958A 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: 4.108A pdb=" N ALA J 149 " --> pdb=" O ALA J 145 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE J 156 " --> pdb=" O TRP J 152 " (cutoff:3.500A) removed outlier: 5.063A 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: 3.764A 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: 6.728A pdb=" N LYS A 129 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 5.743A 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: 8.378A pdb=" N VAL A 59 " --> pdb=" O TRP A 156 " (cutoff:3.500A) removed outlier: 6.310A 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: 6.454A 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: 6.555A pdb=" N PHE A 392 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE A 317 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 6.449A 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: 6.727A pdb=" N LYS E 129 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 5.743A 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: 8.378A pdb=" N VAL E 59 " --> pdb=" O TRP E 156 " (cutoff:3.500A) removed outlier: 6.310A 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: 6.454A 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: 6.555A pdb=" N PHE E 392 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE E 317 " --> pdb=" O LEU E 390 " (cutoff:3.500A) removed outlier: 6.448A 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: 6.728A pdb=" N LYS I 129 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 5.743A 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: 8.377A pdb=" N VAL I 59 " --> pdb=" O TRP I 156 " (cutoff:3.500A) removed outlier: 6.309A 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: 6.454A 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: 6.555A pdb=" N PHE I 392 " --> pdb=" O GLY I 315 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE I 317 " --> pdb=" O LEU I 390 " (cutoff:3.500A) removed outlier: 6.448A 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 1005 hydrogen bonds defined for protein. 2772 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: 7.57 Time building geometry restraints manager: 10.77 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: 3302 1.32 - 1.44: 6807 1.44 - 1.57: 12698 1.57 - 1.69: 140 1.69 - 1.81: 180 Bond restraints: 23127 Sorted by residual: bond pdb=" CB PLC K 301 " pdb=" O3 PLC K 301 " ideal model delta sigma weight residual 1.327 1.455 -0.128 2.00e-02 2.50e+03 4.07e+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 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 4.01e+01 bond pdb=" CB PLC G 303 " pdb=" O3 PLC G 303 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" CB PLC C 302 " pdb=" O3 PLC C 302 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.96e+01 ... (remaining 23122 not shown) Histogram of bond angle deviations from ideal: 98.70 - 105.84: 571 105.84 - 112.98: 12389 112.98 - 120.12: 8441 120.12 - 127.26: 9491 127.26 - 134.40: 401 Bond angle restraints: 31293 Sorted by residual: angle pdb=" N THR G 232 " pdb=" CA THR G 232 " pdb=" C THR G 232 " ideal model delta sigma weight residual 111.03 104.44 6.59 1.11e+00 8.12e-01 3.52e+01 angle pdb=" N THR C 232 " pdb=" CA THR C 232 " pdb=" C THR C 232 " ideal model delta sigma weight residual 111.03 104.48 6.55 1.11e+00 8.12e-01 3.48e+01 angle pdb=" N THR K 232 " pdb=" CA THR K 232 " pdb=" C THR K 232 " ideal model delta sigma weight residual 111.03 104.49 6.54 1.11e+00 8.12e-01 3.47e+01 angle pdb=" N LEU I 376 " pdb=" CA LEU I 376 " pdb=" C LEU I 376 " ideal model delta sigma weight residual 112.89 107.12 5.77 1.24e+00 6.50e-01 2.17e+01 angle pdb=" N LEU E 376 " pdb=" CA LEU E 376 " pdb=" C LEU E 376 " ideal model delta sigma weight residual 112.89 107.12 5.77 1.24e+00 6.50e-01 2.17e+01 ... (remaining 31288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.45: 12582 34.45 - 68.89: 819 68.89 - 103.34: 96 103.34 - 137.78: 36 137.78 - 172.23: 12 Dihedral angle restraints: 13545 sinusoidal: 6093 harmonic: 7452 Sorted by residual: dihedral pdb=" O2 PLC K 301 " pdb=" C1 PLC K 301 " pdb=" C2 PLC K 301 " pdb=" O3P PLC K 301 " ideal model delta sinusoidal sigma weight residual -55.71 116.52 -172.23 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O2 PLC G 301 " pdb=" C1 PLC G 301 " pdb=" C2 PLC G 301 " pdb=" O3P PLC G 301 " ideal model delta sinusoidal sigma weight residual -55.71 116.52 -172.23 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O2 PLC C 310 " pdb=" C1 PLC C 310 " pdb=" C2 PLC C 310 " pdb=" O3P PLC C 310 " ideal model delta sinusoidal sigma weight residual -55.71 116.50 -172.21 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 13542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2376 0.049 - 0.099: 647 0.099 - 0.148: 148 0.148 - 0.198: 25 0.198 - 0.247: 11 Chirality restraints: 3207 Sorted by residual: 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 -2.56 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" C2 PLC G 308 " pdb=" C1 PLC G 308 " pdb=" C3 PLC G 308 " pdb=" O2 PLC G 308 " both_signs ideal model delta sigma weight residual False -2.31 -2.56 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C2 PLC K 308 " pdb=" C1 PLC K 308 " pdb=" C3 PLC K 308 " pdb=" O2 PLC K 308 " both_signs ideal model delta sigma weight residual False -2.31 -2.56 0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 3204 not shown) Planarity restraints: 3732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY E 34 " -0.009 2.00e-02 2.50e+03 1.73e-02 3.01e+00 pdb=" C GLY E 34 " 0.030 2.00e-02 2.50e+03 pdb=" O GLY E 34 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU E 35 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 34 " 0.009 2.00e-02 2.50e+03 1.73e-02 3.00e+00 pdb=" C GLY A 34 " -0.030 2.00e-02 2.50e+03 pdb=" O GLY A 34 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU A 35 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY I 34 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.96e+00 pdb=" C GLY I 34 " -0.030 2.00e-02 2.50e+03 pdb=" O GLY I 34 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU I 35 " 0.010 2.00e-02 2.50e+03 ... (remaining 3729 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 16 2.14 - 2.83: 7322 2.83 - 3.52: 33900 3.52 - 4.21: 64448 4.21 - 4.90: 107434 Nonbonded interactions: 213120 Sorted by model distance: nonbonded pdb=" NE2 HIS C 245 " pdb="CU CU C 301 " model vdw 1.450 2.320 nonbonded pdb=" NE2 HIS K 245 " pdb="CU CU K 302 " model vdw 1.451 2.320 nonbonded pdb=" NE2 HIS G 245 " pdb="CU CU G 302 " model vdw 1.451 2.320 nonbonded pdb=" ND1 HIS E 33 " pdb="CU CU E 501 " model vdw 1.967 2.320 nonbonded pdb=" ND1 HIS A 33 " pdb="CU CU A 501 " model vdw 1.968 2.320 ... (remaining 213115 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = (chain 'B' and (resid 7 through 247 or resid 305 through 306)) selection = (chain 'F' and (resid 7 through 247 or resid 305 through 306)) selection = (chain 'J' and (resid 7 through 247 or resid 305 through 306)) } ncs_group { reference = (chain 'C' and (resid 45 through 280 or resid 309)) selection = (chain 'G' and (resid 45 through 280 or resid 309)) selection = (chain 'K' and (resid 45 through 280 or resid 309)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.230 Construct map_model_manager: 0.020 Extract box with map and model: 17.620 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 61.840 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.160 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:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 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 : 0.008 0.128 23127 Z= 0.520 Angle : 1.010 10.610 31293 Z= 0.478 Chirality : 0.049 0.247 3207 Planarity : 0.005 0.043 3732 Dihedral : 22.635 172.228 8787 Min Nonbonded Distance : 1.450 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.24 % Favored : 94.29 % Rotamer: Outliers : 3.29 % Allowed : 18.06 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.17), residues: 2559 helix: 1.19 (0.15), residues: 1200 sheet: 1.30 (0.28), residues: 357 loop : -0.45 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 202 HIS 0.021 0.002 HIS A 33 PHE 0.015 0.001 PHE J 31 TYR 0.021 0.001 TYR C 184 ARG 0.005 0.000 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 322 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 250 time to evaluate : 2.555 Fit side-chains REVERT: A 108 GLN cc_start: 0.8068 (pt0) cc_final: 0.7772 (pp30) REVERT: C 45 LEU cc_start: 0.6594 (OUTLIER) cc_final: 0.6374 (mt) REVERT: G 45 LEU cc_start: 0.6593 (OUTLIER) cc_final: 0.6384 (mt) REVERT: K 45 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6384 (mt) REVERT: E 108 GLN cc_start: 0.8056 (pt0) cc_final: 0.7772 (pp30) REVERT: I 108 GLN cc_start: 0.8039 (pt0) cc_final: 0.7739 (pp30) REVERT: I 399 ASN cc_start: 0.7495 (p0) cc_final: 0.7290 (p0) REVERT: J 172 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7752 (tp30) outliers start: 72 outliers final: 39 residues processed: 313 average time/residue: 1.5637 time to fit residues: 552.0808 Evaluate side-chains 273 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 231 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 256 SER Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain C residue 240 PHE 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 138 SER Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 207 SER Chi-restraints excluded: chain G residue 231 HIS Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 207 SER Chi-restraints excluded: chain K residue 231 HIS Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 256 SER Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 138 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 215 optimal weight: 5.9990 chunk 193 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 199 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 231 optimal weight: 20.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 ASN G 118 ASN K 118 ASN E 168 ASN E 404 GLN I 168 ASN I 404 GLN F 187 ASN J 187 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 23127 Z= 0.295 Angle : 0.662 7.179 31293 Z= 0.341 Chirality : 0.049 0.382 3207 Planarity : 0.005 0.037 3732 Dihedral : 22.642 175.895 4211 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.85 % Favored : 94.92 % Rotamer: Outliers : 3.75 % Allowed : 16.19 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.17), residues: 2559 helix: 1.02 (0.15), residues: 1239 sheet: 0.97 (0.27), residues: 372 loop : -0.22 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP G 234 HIS 0.005 0.001 HIS E 192 PHE 0.020 0.002 PHE B 31 TYR 0.022 0.002 TYR G 184 ARG 0.006 0.001 ARG K 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 222 time to evaluate : 2.434 Fit side-chains REVERT: A 108 GLN cc_start: 0.8122 (pt0) cc_final: 0.7820 (pp30) REVERT: A 112 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8127 (mtt180) REVERT: A 316 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7643 (tt0) REVERT: G 196 LYS cc_start: 0.9352 (OUTLIER) cc_final: 0.8824 (tttm) REVERT: E 108 GLN cc_start: 0.8113 (pt0) cc_final: 0.7817 (pp30) REVERT: E 112 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8167 (mtt180) REVERT: E 316 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7678 (tt0) REVERT: I 108 GLN cc_start: 0.8092 (pt0) cc_final: 0.7819 (pp30) REVERT: I 112 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8187 (mtt180) REVERT: J 13 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8112 (tt0) outliers start: 82 outliers final: 34 residues processed: 284 average time/residue: 1.5663 time to fit residues: 501.4343 Evaluate side-chains 261 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 220 time to evaluate : 2.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 112 ARG Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 196 LYS Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 176 GLN Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 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 J residue 13 GLU Chi-restraints excluded: chain J residue 59 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 128 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 chunk 157 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 231 optimal weight: 20.0000 chunk 250 optimal weight: 6.9990 chunk 206 optimal weight: 3.9990 chunk 230 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 186 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 118 ASN G 118 ASN K 118 ASN E 168 ASN E 404 GLN I 168 ASN ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 ASN J 187 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 23127 Z= 0.336 Angle : 0.679 9.121 31293 Z= 0.352 Chirality : 0.049 0.297 3207 Planarity : 0.005 0.039 3732 Dihedral : 21.846 171.139 4176 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.88 % Favored : 94.76 % Rotamer: Outliers : 3.43 % Allowed : 16.19 % Favored : 80.38 % 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: 0.65 (0.17), residues: 2559 helix: 0.94 (0.15), residues: 1236 sheet: 0.69 (0.26), residues: 387 loop : -0.22 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 234 HIS 0.005 0.001 HIS E 192 PHE 0.022 0.002 PHE B 31 TYR 0.023 0.002 TYR G 184 ARG 0.007 0.001 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 312 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 237 time to evaluate : 2.791 Fit side-chains REVERT: A 108 GLN cc_start: 0.8094 (pt0) cc_final: 0.7796 (pp30) REVERT: A 112 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8155 (mtt180) REVERT: A 316 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7654 (tt0) REVERT: A 403 VAL cc_start: 0.9069 (OUTLIER) cc_final: 0.8853 (t) REVERT: C 196 LYS cc_start: 0.9359 (OUTLIER) cc_final: 0.8616 (ttmm) REVERT: C 235 PHE cc_start: 0.7101 (m-80) cc_final: 0.6889 (m-80) REVERT: K 45 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6715 (mt) REVERT: E 108 GLN cc_start: 0.8099 (pt0) cc_final: 0.7809 (pp30) REVERT: E 112 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8187 (mtt180) REVERT: E 316 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7687 (tt0) REVERT: E 403 VAL cc_start: 0.9085 (OUTLIER) cc_final: 0.8869 (t) REVERT: I 112 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8251 (mtt180) REVERT: I 163 MET cc_start: 0.8614 (ttt) cc_final: 0.8313 (ttt) REVERT: I 403 VAL cc_start: 0.9093 (OUTLIER) cc_final: 0.8860 (t) outliers start: 75 outliers final: 37 residues processed: 295 average time/residue: 1.5913 time to fit residues: 527.6762 Evaluate side-chains 274 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 227 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL 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 316 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 274 LEU Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 176 GLN Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 403 VAL 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 J residue 8 VAL Chi-restraints excluded: chain J residue 59 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 229 optimal weight: 0.7980 chunk 174 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 232 optimal weight: 9.9990 chunk 246 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 220 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 118 ASN G 118 ASN K 118 ASN E 168 ASN E 404 GLN I 168 ASN I 176 GLN I 404 GLN F 187 ASN J 187 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23127 Z= 0.273 Angle : 0.625 8.692 31293 Z= 0.323 Chirality : 0.047 0.286 3207 Planarity : 0.005 0.037 3732 Dihedral : 21.233 172.048 4171 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.77 % Favored : 95.12 % Rotamer: Outliers : 3.43 % Allowed : 16.14 % Favored : 80.43 % 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: 0.74 (0.17), residues: 2559 helix: 1.01 (0.15), residues: 1236 sheet: 0.71 (0.27), residues: 384 loop : -0.15 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 231 HIS 0.004 0.001 HIS J 11 PHE 0.020 0.002 PHE J 31 TYR 0.022 0.002 TYR G 184 ARG 0.009 0.000 ARG K 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 237 time to evaluate : 2.636 Fit side-chains REVERT: A 108 GLN cc_start: 0.8058 (pt0) cc_final: 0.7756 (pp30) REVERT: A 316 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7642 (tt0) REVERT: C 196 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.8602 (ttmm) REVERT: K 45 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6689 (mt) REVERT: E 108 GLN cc_start: 0.8078 (pt0) cc_final: 0.7773 (pp30) REVERT: E 316 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7706 (tt0) REVERT: I 108 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7769 (pp30) REVERT: I 112 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8175 (mtt180) REVERT: I 163 MET cc_start: 0.8624 (ttt) cc_final: 0.8386 (ttt) REVERT: F 198 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8329 (ttp-170) outliers start: 75 outliers final: 33 residues processed: 298 average time/residue: 1.5876 time to fit residues: 532.3195 Evaluate side-chains 269 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 229 time to evaluate : 2.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 196 LYS 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 G residue 123 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain K residue 274 LEU Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 108 GLN Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain 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 198 ARG Chi-restraints excluded: chain J residue 59 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 205 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 183 optimal weight: 0.4980 chunk 101 optimal weight: 6.9990 chunk 210 optimal weight: 7.9990 chunk 170 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 125 optimal weight: 0.7980 chunk 221 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- 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 118 ASN G 118 ASN K 118 ASN E 168 ASN E 404 GLN I 168 ASN I 404 GLN F 187 ASN J 187 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23127 Z= 0.257 Angle : 0.615 8.482 31293 Z= 0.319 Chirality : 0.047 0.271 3207 Planarity : 0.005 0.038 3732 Dihedral : 20.674 173.995 4167 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.92 % Favored : 94.96 % Rotamer: Outliers : 3.52 % Allowed : 15.96 % Favored : 80.52 % 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: 0.74 (0.17), residues: 2559 helix: 0.99 (0.15), residues: 1239 sheet: 0.68 (0.26), residues: 384 loop : -0.12 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 231 HIS 0.004 0.001 HIS J 11 PHE 0.020 0.002 PHE B 31 TYR 0.022 0.002 TYR G 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 313 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 236 time to evaluate : 2.293 Fit side-chains REVERT: A 108 GLN cc_start: 0.8036 (pt0) cc_final: 0.7774 (pp30) REVERT: A 112 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8145 (mtt180) REVERT: A 316 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7638 (tt0) REVERT: C 196 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.8583 (ttmm) REVERT: E 108 GLN cc_start: 0.8066 (pt0) cc_final: 0.7802 (pp30) REVERT: E 112 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8180 (mtt180) REVERT: E 316 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7660 (tt0) REVERT: E 403 VAL cc_start: 0.9096 (OUTLIER) cc_final: 0.8870 (t) REVERT: I 108 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7739 (pp30) REVERT: I 163 MET cc_start: 0.8620 (ttt) cc_final: 0.8378 (ttt) REVERT: F 198 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8355 (ttp-170) REVERT: J 198 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.7564 (ttp-170) outliers start: 77 outliers final: 44 residues processed: 297 average time/residue: 1.6138 time to fit residues: 541.3150 Evaluate side-chains 282 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 229 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL 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 316 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain G residue 113 LYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 274 LEU 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 65 VAL Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 108 GLN Chi-restraints excluded: chain I residue 176 GLN Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 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 59 LEU Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 198 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 82 optimal weight: 10.0000 chunk 221 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 144 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 246 optimal weight: 2.9990 chunk 204 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 118 ASN G 118 ASN K 118 ASN E 168 ASN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 176 GLN ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23127 Z= 0.250 Angle : 0.605 8.410 31293 Z= 0.314 Chirality : 0.046 0.266 3207 Planarity : 0.005 0.039 3732 Dihedral : 20.305 174.233 4165 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.92 % Favored : 94.96 % Rotamer: Outliers : 3.34 % Allowed : 15.96 % Favored : 80.70 % 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: 0.98 (0.15), residues: 1248 sheet: 0.92 (0.27), residues: 369 loop : -0.10 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 231 HIS 0.004 0.001 HIS E 192 PHE 0.019 0.002 PHE B 31 TYR 0.022 0.002 TYR G 184 ARG 0.010 0.000 ARG G 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 307 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 234 time to evaluate : 2.869 Fit side-chains REVERT: A 112 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8119 (mtt180) REVERT: A 316 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7640 (tt0) REVERT: C 196 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.8577 (ttmm) REVERT: E 112 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8160 (mtt180) REVERT: E 316 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7654 (tt0) REVERT: I 108 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7736 (pp30) REVERT: I 112 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8204 (mtt180) REVERT: I 163 MET cc_start: 0.8622 (ttt) cc_final: 0.8395 (ttt) REVERT: I 299 ARG cc_start: 0.7401 (ttp80) cc_final: 0.6993 (ptm-80) REVERT: F 198 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8334 (ttp-170) REVERT: J 198 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.7571 (ttp-170) outliers start: 73 outliers final: 40 residues processed: 296 average time/residue: 1.6519 time to fit residues: 548.9788 Evaluate side-chains 274 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 225 time to evaluate : 2.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL 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 316 GLU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 214 VAL 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 65 VAL Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 108 GLN Chi-restraints excluded: chain I residue 112 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain 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 198 ARG Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 198 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 237 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 180 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 chunk 207 optimal weight: 0.0970 chunk 137 optimal weight: 2.9990 chunk 245 optimal weight: 7.9990 chunk 153 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 ASN G 118 ASN K 118 ASN E 168 ASN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN I 176 GLN I 404 GLN F 187 ASN J 187 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23127 Z= 0.160 Angle : 0.552 7.591 31293 Z= 0.283 Chirality : 0.045 0.252 3207 Planarity : 0.004 0.041 3732 Dihedral : 19.762 177.588 4165 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.88 % Favored : 95.00 % Rotamer: Outliers : 2.83 % Allowed : 16.64 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.17), residues: 2559 helix: 1.14 (0.15), residues: 1233 sheet: 0.99 (0.27), residues: 369 loop : -0.10 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 206 HIS 0.003 0.001 HIS C 245 PHE 0.016 0.001 PHE B 31 TYR 0.020 0.001 TYR C 184 ARG 0.009 0.000 ARG K 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 299 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 237 time to evaluate : 2.662 Fit side-chains REVERT: A 288 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7688 (p0) REVERT: A 316 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7572 (tt0) REVERT: A 399 ASN cc_start: 0.7637 (p0) cc_final: 0.7437 (p0) REVERT: C 196 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8507 (ttmm) REVERT: B 245 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7711 (mm110) REVERT: E 288 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7614 (p0) REVERT: E 316 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7611 (tt0) REVERT: I 108 GLN cc_start: 0.7910 (pp30) cc_final: 0.7663 (pp30) REVERT: I 299 ARG cc_start: 0.7365 (ttp80) cc_final: 0.6994 (ptm-80) REVERT: I 363 ASP cc_start: 0.7841 (m-30) cc_final: 0.7609 (m-30) REVERT: F 198 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8213 (ttp-170) outliers start: 62 outliers final: 34 residues processed: 290 average time/residue: 1.6075 time to fit residues: 524.0948 Evaluate side-chains 271 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 231 time to evaluate : 2.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain G residue 113 LYS Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 263 THR 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 227 LEU Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain 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 137 LEU Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 29 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 152 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 156 optimal weight: 9.9990 chunk 167 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 193 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 ASN G 118 ASN K 118 ASN E 168 ASN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN I 176 GLN ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 ASN J 187 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23127 Z= 0.289 Angle : 0.623 8.640 31293 Z= 0.323 Chirality : 0.047 0.264 3207 Planarity : 0.005 0.038 3732 Dihedral : 19.871 174.806 4159 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.35 % Favored : 94.53 % Rotamer: Outliers : 3.02 % Allowed : 16.05 % Favored : 80.93 % 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: 1.03 (0.15), residues: 1245 sheet: 0.70 (0.27), residues: 384 loop : -0.06 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 231 HIS 0.005 0.001 HIS E 192 PHE 0.020 0.002 PHE B 31 TYR 0.023 0.002 TYR G 184 ARG 0.008 0.000 ARG K 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 291 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 225 time to evaluate : 2.510 Fit side-chains REVERT: A 112 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8235 (mtt180) REVERT: A 316 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7633 (tt0) REVERT: C 196 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.8572 (ttmm) REVERT: E 112 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8249 (mtt180) REVERT: E 316 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: I 108 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7698 (pp30) REVERT: I 288 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7799 (p0) REVERT: I 299 ARG cc_start: 0.7392 (ttp80) cc_final: 0.6944 (ptm-80) REVERT: I 363 ASP cc_start: 0.7858 (m-30) cc_final: 0.7625 (m-30) outliers start: 66 outliers final: 41 residues processed: 280 average time/residue: 1.6072 time to fit residues: 505.9756 Evaluate side-chains 272 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 224 time to evaluate : 2.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL 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 316 GLU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 108 GLN Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain 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 137 LEU Chi-restraints excluded: chain J residue 59 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 223 optimal weight: 0.5980 chunk 235 optimal weight: 3.9990 chunk 214 optimal weight: 0.7980 chunk 229 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 179 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 206 optimal weight: 4.9990 chunk 216 optimal weight: 7.9990 chunk 228 optimal weight: 6.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 118 ASN G 118 ASN K 118 ASN E 168 ASN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN I 176 GLN ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 ASN J 187 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1610 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= 0.244 Angle : 0.606 8.329 31293 Z= 0.313 Chirality : 0.047 0.262 3207 Planarity : 0.005 0.041 3732 Dihedral : 19.678 175.342 4159 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.77 % Favored : 95.12 % Rotamer: Outliers : 2.56 % Allowed : 16.51 % Favored : 80.93 % 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: 0.87 (0.17), residues: 2559 helix: 1.04 (0.15), residues: 1242 sheet: 0.93 (0.27), residues: 369 loop : -0.05 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 231 HIS 0.004 0.001 HIS E 192 PHE 0.019 0.002 PHE B 31 TYR 0.022 0.002 TYR G 184 ARG 0.009 0.000 ARG G 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 227 time to evaluate : 2.475 Fit side-chains REVERT: A 112 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8236 (mtt180) REVERT: A 316 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7624 (tt0) REVERT: C 196 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.8566 (ttmm) REVERT: E 112 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8239 (mtt180) REVERT: E 316 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7654 (tt0) REVERT: I 108 GLN cc_start: 0.7993 (pp30) cc_final: 0.7695 (pp30) REVERT: I 288 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7747 (p0) REVERT: I 299 ARG cc_start: 0.7388 (ttp80) cc_final: 0.6956 (ptm-80) REVERT: I 363 ASP cc_start: 0.7852 (m-30) cc_final: 0.7620 (m-30) REVERT: F 198 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8360 (ttp-170) outliers start: 56 outliers final: 41 residues processed: 278 average time/residue: 1.6240 time to fit residues: 506.8714 Evaluate side-chains 272 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 224 time to evaluate : 2.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL 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 316 GLU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 240 PHE Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain 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 137 LEU Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 59 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 150 optimal weight: 0.0060 chunk 242 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 chunk 254 optimal weight: 1.9990 chunk 233 optimal weight: 2.9990 chunk 202 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 ASN B 187 ASN G 118 ASN K 118 ASN E 168 ASN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN I 176 GLN ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 ASN J 187 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23127 Z= 0.176 Angle : 0.569 8.137 31293 Z= 0.291 Chirality : 0.045 0.253 3207 Planarity : 0.004 0.041 3732 Dihedral : 19.190 178.141 4159 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.00 % Favored : 94.88 % Rotamer: Outliers : 2.19 % Allowed : 16.96 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.17), residues: 2559 helix: 1.15 (0.15), residues: 1233 sheet: 0.96 (0.27), residues: 369 loop : -0.05 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 231 HIS 0.003 0.001 HIS G 245 PHE 0.017 0.001 PHE B 31 TYR 0.021 0.001 TYR G 184 ARG 0.010 0.000 ARG K 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 278 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 230 time to evaluate : 2.880 Fit side-chains REVERT: A 316 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: C 196 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.8526 (ttmm) REVERT: E 316 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7612 (tt0) REVERT: I 108 GLN cc_start: 0.7938 (pp30) cc_final: 0.7686 (pp30) REVERT: I 288 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7697 (p0) REVERT: I 299 ARG cc_start: 0.7362 (ttp80) cc_final: 0.7013 (ptm-80) REVERT: F 198 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8129 (ttp-170) outliers start: 48 outliers final: 35 residues processed: 274 average time/residue: 1.6256 time to fit residues: 501.0378 Evaluate side-chains 268 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 228 time to evaluate : 2.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 214 VAL Chi-restraints excluded: chain K residue 240 PHE Chi-restraints excluded: chain K residue 263 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 403 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 137 LEU Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 59 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 160 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 186 optimal weight: 3.9990 chunk 29 optimal weight: 0.0070 chunk 56 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 208 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 overall best weight: 4.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 ASN B 187 ASN G 118 ASN K 118 ASN E 168 ASN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN I 176 GLN ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 ASN J 187 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.116846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.092743 restraints weight = 24359.084| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.19 r_work: 0.2906 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 23127 Z= 0.368 Angle : 0.680 9.198 31293 Z= 0.353 Chirality : 0.049 0.271 3207 Planarity : 0.005 0.040 3732 Dihedral : 19.534 174.268 4159 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.16 % Favored : 94.61 % Rotamer: Outliers : 2.29 % Allowed : 16.87 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.17), residues: 2559 helix: 0.99 (0.15), residues: 1239 sheet: 0.68 (0.27), residues: 384 loop : -0.10 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 231 HIS 0.006 0.001 HIS E 192 PHE 0.023 0.002 PHE B 31 TYR 0.024 0.002 TYR B 188 ARG 0.010 0.001 ARG K 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9177.91 seconds wall clock time: 164 minutes 57.56 seconds (9897.56 seconds total)