Starting phenix.real_space_refine on Mon Mar 25 03:00:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqw_40714/03_2024/8sqw_40714_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqw_40714/03_2024/8sqw_40714.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqw_40714/03_2024/8sqw_40714.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqw_40714/03_2024/8sqw_40714.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqw_40714/03_2024/8sqw_40714_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sqw_40714/03_2024/8sqw_40714_trim_updated.pdb" } resolution = 2.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 20898 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: 7 Type Number sf(0) Gaussians Cu 9 5.60 5 P 36 5.49 5 S 93 5.16 5 C 15036 2.51 5 N 3417 2.21 5 O 4250 1.98 5 F 9 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 406": "OD1" <-> "OD2" Residue "C ARG 165": "NH1" <-> "NH2" Residue "C PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 228": "OE1" <-> "OE2" Residue "E PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 406": "OD1" <-> "OD2" Residue "I PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 165": "NH1" <-> "NH2" Residue "G PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 228": "OE1" <-> "OE2" Residue "K ARG 165": "NH1" <-> "NH2" Residue "K PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 228": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22850 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: "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: "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: "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: "G" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1972 Classifications: {'peptide': 236} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain: "K" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1972 Classifications: {'peptide': 236} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' CU': 2, 'D10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "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: "C" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 321 Unusual residues: {' CU': 1, 'D10': 1, 'ETF': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} 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: "G" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 321 Unusual residues: {' CU': 1, 'D10': 1, 'ETF': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "K" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 321 Unusual residues: {' CU': 1, 'D10': 1, 'ETF': 1, 'HXG': 2, 'P1O': 2, 'PLC': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} 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: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} 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: "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} Chain: "G" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "K" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Time building chain proxies: 11.66, per 1000 atoms: 0.51 Number of scatterers: 22850 At special positions: 0 Unit cell: (106.878, 108.995, 119.577, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cu 9 28.99 S 93 16.00 P 36 15.00 F 9 9.00 O 4250 8.00 N 3417 7.00 C 15036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.50 Conformation dependent library (CDL) restraints added in 3.3 seconds 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4758 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 78 helices and 24 sheets defined 45.9% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.61 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: 3.630A pdb=" N ILE A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 44 Processing helix chain 'B' and resid 46 through 50 Processing helix chain 'B' and resid 59 through 83 Proline residue: B 65 - end of helix removed outlier: 4.442A pdb=" N THR B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 5.419A 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: 3.779A pdb=" N PHE B 156 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 5.063A 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: 3.763A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 72 removed outlier: 3.905A 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 154 No H-bonds generated for 'chain 'C' and resid 151 through 154' Processing helix chain 'C' and resid 182 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: 4.453A pdb=" N LEU C 226 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 269 removed outlier: 5.042A pdb=" N GLY C 247 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL C 249 " --> pdb=" O TYR C 246 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE C 250 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE C 251 " --> pdb=" O PHE C 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: 3.631A 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: 3.630A 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: 4.441A 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: 3.958A 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: 4.109A pdb=" N ALA F 149 " --> pdb=" O ALA F 145 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE F 156 " --> pdb=" O TRP F 152 " (cutoff:3.500A) removed outlier: 5.063A 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: 3.764A 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: 4.442A pdb=" N THR J 70 " --> pdb=" O ILE J 66 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N PHE J 71 " --> pdb=" O VAL J 67 " (cutoff:3.500A) Proline residue: J 72 - end of helix removed outlier: 3.957A 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: 4.109A pdb=" N ALA J 149 " --> pdb=" O ALA J 145 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE J 156 " --> pdb=" O TRP J 152 " (cutoff:3.500A) removed outlier: 5.064A 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 helix chain 'G' and resid 50 through 72 removed outlier: 3.905A 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 154 No H-bonds generated for 'chain 'G' and resid 151 through 154' Processing helix chain 'G' and resid 182 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: 4.341A 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: 4.453A pdb=" N LEU G 226 " --> pdb=" O PRO G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 269 removed outlier: 5.042A pdb=" N GLY G 247 " --> pdb=" O LEU G 244 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL G 249 " --> pdb=" O TYR G 246 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE G 250 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE G 251 " --> pdb=" O PHE G 248 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 72 removed outlier: 3.905A 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 154 No H-bonds generated for 'chain 'K' and resid 151 through 154' Processing helix chain 'K' and resid 182 through 198 Processing helix chain 'K' and resid 208 through 232 Proline residue: K 217 - end of helix removed outlier: 3.578A 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: 4.662A pdb=" N GLY K 225 " --> pdb=" O LEU K 221 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU K 226 " --> pdb=" O PRO K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 243 through 269 removed outlier: 5.042A pdb=" N GLY K 247 " --> pdb=" O LEU K 244 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL K 249 " --> pdb=" O TYR K 246 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE K 250 " --> pdb=" O GLY K 247 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE K 251 " --> pdb=" O PHE K 248 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 47 through 50 removed outlier: 6.730A pdb=" N LYS A 129 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 5.744A 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: 6.312A 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: 6.453A 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: 6.554A 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: 6.448A 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: 6.731A pdb=" N LYS E 129 " --> pdb=" O ARG E 100 " (cutoff:3.500A) removed outlier: 5.742A 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: 8.377A pdb=" N VAL E 59 " --> pdb=" O TRP E 156 " (cutoff:3.500A) removed outlier: 6.311A 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: 6.453A 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: 6.553A 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: 6.729A pdb=" N LYS I 129 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 5.744A 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: 6.310A 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: 6.451A 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: 6.553A pdb=" N PHE I 392 " --> pdb=" O GLY I 315 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHE I 317 " --> pdb=" O LEU I 390 " (cutoff:3.500A) removed outlier: 6.450A 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 173 975 hydrogen bonds defined for protein. 2691 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: 7.14 Time building geometry restraints manager: 10.09 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: 3368 1.32 - 1.44: 6755 1.44 - 1.57: 12701 1.57 - 1.69: 138 1.69 - 1.81: 180 Bond restraints: 23142 Sorted by residual: 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 4.00e+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 3.95e+01 bond pdb=" CB PLC K 303 " pdb=" O3 PLC K 303 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" CB PLC G 301 " pdb=" O3 PLC G 301 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" CB PLC C 311 " pdb=" O3 PLC C 311 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.94e+01 ... (remaining 23137 not shown) Histogram of bond angle deviations from ideal: 98.69 - 105.86: 601 105.86 - 113.03: 12408 113.03 - 120.20: 8595 120.20 - 127.37: 9321 127.37 - 134.54: 389 Bond angle restraints: 31314 Sorted by residual: angle pdb=" C PHE G 248 " pdb=" N VAL G 249 " pdb=" CA VAL G 249 " ideal model delta sigma weight residual 120.56 109.66 10.90 1.28e+00 6.10e-01 7.25e+01 angle pdb=" C PHE K 248 " pdb=" N VAL K 249 " pdb=" CA VAL K 249 " ideal model delta sigma weight residual 120.56 109.67 10.89 1.28e+00 6.10e-01 7.24e+01 angle pdb=" C PHE C 248 " pdb=" N VAL C 249 " pdb=" CA VAL C 249 " ideal model delta sigma weight residual 120.56 109.68 10.88 1.28e+00 6.10e-01 7.23e+01 angle pdb=" N PHE G 248 " pdb=" CA PHE G 248 " pdb=" C PHE G 248 " ideal model delta sigma weight residual 112.23 102.93 9.30 1.26e+00 6.30e-01 5.45e+01 angle pdb=" N PHE C 248 " pdb=" CA PHE C 248 " pdb=" C PHE C 248 " ideal model delta sigma weight residual 112.23 102.95 9.28 1.26e+00 6.30e-01 5.42e+01 ... (remaining 31309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.44: 12593 34.44 - 68.89: 808 68.89 - 103.33: 99 103.33 - 137.77: 36 137.77 - 172.21: 12 Dihedral angle restraints: 13548 sinusoidal: 6096 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 -55.71 116.50 -172.21 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 -55.71 116.49 -172.20 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O2 PLC C 311 " pdb=" C1 PLC C 311 " pdb=" C2 PLC C 311 " pdb=" O3P PLC C 311 " ideal model delta sinusoidal sigma weight residual -55.71 116.47 -172.18 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 13545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2378 0.052 - 0.104: 639 0.104 - 0.155: 129 0.155 - 0.207: 46 0.207 - 0.259: 15 Chirality restraints: 3207 Sorted by residual: chirality pdb=" CA TYR K 246 " pdb=" N TYR K 246 " pdb=" C TYR K 246 " pdb=" CB TYR K 246 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA TYR G 246 " pdb=" N TYR G 246 " pdb=" C TYR G 246 " pdb=" CB TYR G 246 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA TYR C 246 " pdb=" N TYR C 246 " pdb=" C TYR C 246 " pdb=" CB TYR C 246 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 3204 not shown) Planarity restraints: 3732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 165 " 0.634 9.50e-02 1.11e+02 2.84e-01 4.97e+01 pdb=" NE ARG G 165 " -0.041 2.00e-02 2.50e+03 pdb=" CZ ARG G 165 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG G 165 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG G 165 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 165 " -0.634 9.50e-02 1.11e+02 2.84e-01 4.97e+01 pdb=" NE ARG K 165 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG K 165 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG K 165 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG K 165 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 165 " -0.634 9.50e-02 1.11e+02 2.84e-01 4.97e+01 pdb=" NE ARG C 165 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG C 165 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 165 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 165 " -0.019 2.00e-02 2.50e+03 ... (remaining 3729 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.29: 54 2.29 - 2.95: 10890 2.95 - 3.60: 36231 3.60 - 4.25: 63916 4.25 - 4.90: 102659 Nonbonded interactions: 213750 Sorted by model distance: nonbonded pdb=" NE2 HIS K 245 " pdb="CU CU K 302 " model vdw 1.642 2.320 nonbonded pdb=" NE2 HIS C 245 " pdb="CU CU C 301 " model vdw 1.643 2.320 nonbonded pdb=" NE2 HIS G 245 " pdb="CU CU G 302 " model vdw 1.643 2.320 nonbonded pdb=" F2 ETF C 310 " pdb=" O HOH C 402 " model vdw 1.861 2.390 nonbonded pdb=" F2 ETF C 310 " pdb=" O HOH C 401 " model vdw 1.875 2.390 ... (remaining 213745 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 304 through 306)) selection = (chain 'F' and (resid 7 through 247 or resid 304 through 306)) selection = (chain 'J' and (resid 7 through 247 or resid 304 through 306)) } ncs_group { reference = (chain 'C' and (resid 45 through 280 or resid 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: 8.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.270 Construct map_model_manager: 0.020 Extract box with map and model: 27.780 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 57.730 Find NCS groups from input model: 1.330 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:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.126 23142 Z= 0.534 Angle : 1.087 10.896 31314 Z= 0.560 Chirality : 0.054 0.259 3207 Planarity : 0.009 0.284 3732 Dihedral : 22.730 172.214 8790 Min Nonbonded Distance : 1.642 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.10 % Favored : 93.32 % Rotamer: Outliers : 4.12 % Allowed : 17.70 % Favored : 78.19 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.17), residues: 2559 helix: 1.05 (0.16), residues: 1182 sheet: 1.30 (0.28), residues: 357 loop : -0.71 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 202 HIS 0.049 0.004 HIS C 245 PHE 0.020 0.002 PHE K 240 TYR 0.040 0.002 TYR G 178 ARG 0.006 0.001 ARG G 165 *********************** 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 500 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 410 time to evaluate : 2.656 Fit side-chains revert: symmetry clash REVERT: K 165 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7194 (mtt90) outliers start: 90 outliers final: 27 residues processed: 486 average time/residue: 1.3715 time to fit residues: 757.6668 Evaluate side-chains 302 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 274 time to evaluate : 2.374 ------------------------------------------------------------------------------- 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 309 ASN Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 231 HIS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 231 HIS Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 165 ARG Chi-restraints excluded: chain K residue 231 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 215 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 chunk 107 optimal weight: 0.0030 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 148 optimal weight: 8.9990 chunk 231 optimal weight: 3.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN E 38 GLN G 155 GLN K 91 ASN K 155 GLN K 276 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23142 Z= 0.234 Angle : 0.665 9.881 31314 Z= 0.333 Chirality : 0.046 0.316 3207 Planarity : 0.005 0.038 3732 Dihedral : 22.389 179.222 4205 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.00 % Favored : 94.88 % Rotamer: Outliers : 4.30 % Allowed : 19.25 % Favored : 76.45 % 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: 0.97 (0.15), residues: 1224 sheet: 1.20 (0.28), residues: 357 loop : -0.47 (0.21), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP K 234 HIS 0.006 0.001 HIS C 160 PHE 0.021 0.002 PHE J 31 TYR 0.021 0.002 TYR C 184 ARG 0.007 0.001 ARG C 165 *********************** 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 403 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 309 time to evaluate : 2.624 Fit side-chains revert: symmetry clash REVERT: A 227 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7160 (mp) REVERT: B 11 HIS cc_start: 0.7060 (m-70) cc_final: 0.6842 (m-70) REVERT: C 214 VAL cc_start: 0.7902 (OUTLIER) cc_final: 0.7634 (p) REVERT: C 235 PHE cc_start: 0.6950 (OUTLIER) cc_final: 0.6731 (t80) REVERT: I 227 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.6893 (mp) REVERT: G 130 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7244 (mtt90) REVERT: G 156 ASP cc_start: 0.6489 (OUTLIER) cc_final: 0.6045 (m-30) REVERT: G 235 PHE cc_start: 0.6952 (OUTLIER) cc_final: 0.6661 (t80) REVERT: K 130 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7111 (mtt90) REVERT: K 156 ASP cc_start: 0.6464 (OUTLIER) cc_final: 0.5851 (m-30) REVERT: K 176 GLU cc_start: 0.7415 (tt0) cc_final: 0.7170 (tt0) REVERT: K 214 VAL cc_start: 0.7914 (OUTLIER) cc_final: 0.7637 (p) outliers start: 94 outliers final: 38 residues processed: 371 average time/residue: 1.3849 time to fit residues: 585.7311 Evaluate side-chains 327 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 279 time to evaluate : 2.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 319 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 C residue 45 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 319 THR Chi-restraints excluded: chain I residue 414 MET Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 33 ILE 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 29 VAL Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 130 ARG Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 235 PHE Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 130 ARG Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 214 VAL 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: 7.9990 chunk 192 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 231 optimal weight: 4.9990 chunk 250 optimal weight: 8.9990 chunk 206 optimal weight: 6.9990 chunk 230 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 186 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 ASN K 91 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 23142 Z= 0.407 Angle : 0.734 9.774 31314 Z= 0.378 Chirality : 0.049 0.254 3207 Planarity : 0.005 0.064 3732 Dihedral : 21.283 178.409 4182 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.88 % Favored : 94.88 % Rotamer: Outliers : 5.03 % Allowed : 17.24 % Favored : 77.73 % 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: 0.48 (0.17), residues: 2559 helix: 0.86 (0.15), residues: 1221 sheet: 1.04 (0.28), residues: 357 loop : -0.57 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP J 231 HIS 0.008 0.002 HIS C 160 PHE 0.024 0.003 PHE F 31 TYR 0.028 0.002 TYR C 184 ARG 0.015 0.001 ARG F 206 *********************** 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 400 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 290 time to evaluate : 2.406 Fit side-chains revert: symmetry clash REVERT: A 227 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7300 (mp) REVERT: A 339 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7005 (p0) REVERT: B 198 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8327 (ttp80) REVERT: C 235 PHE cc_start: 0.6932 (OUTLIER) cc_final: 0.6531 (t80) REVERT: E 45 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.6970 (mtp85) REVERT: E 227 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7057 (mp) REVERT: I 45 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.6912 (mtp85) REVERT: I 167 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.6541 (mmp80) REVERT: I 185 GLU cc_start: 0.7674 (tt0) cc_final: 0.7408 (tt0) REVERT: I 227 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7200 (mp) REVERT: F 198 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7944 (ttp80) REVERT: J 198 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8131 (ttp80) REVERT: G 130 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7502 (mtp85) REVERT: G 156 ASP cc_start: 0.6435 (OUTLIER) cc_final: 0.5261 (m-30) REVERT: G 235 PHE cc_start: 0.7002 (OUTLIER) cc_final: 0.6572 (t80) REVERT: K 130 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7233 (mtt90) REVERT: K 156 ASP cc_start: 0.6314 (OUTLIER) cc_final: 0.5393 (m-30) outliers start: 110 outliers final: 43 residues processed: 364 average time/residue: 1.3722 time to fit residues: 569.0215 Evaluate side-chains 323 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 264 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 339 ASP 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 198 ARG Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 298 MET Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 167 ARG Chi-restraints excluded: chain I residue 207 SER 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 F residue 8 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 198 ARG Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 130 ARG Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 235 PHE Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 130 ARG Chi-restraints excluded: chain K residue 156 ASP 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: 6.9990 chunk 120 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 155 optimal weight: 9.9990 chunk 232 optimal weight: 9.9990 chunk 246 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 chunk 220 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN B 174 ASN B 187 ASN C 155 GLN I 168 ASN ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN J 174 ASN J 187 ASN G 155 GLN K 91 ASN K 155 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23142 Z= 0.216 Angle : 0.620 8.577 31314 Z= 0.315 Chirality : 0.045 0.219 3207 Planarity : 0.005 0.074 3732 Dihedral : 20.413 170.949 4176 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.53 % Favored : 95.27 % Rotamer: Outliers : 4.57 % Allowed : 18.06 % Favored : 77.37 % 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: 0.59 (0.17), residues: 2559 helix: 0.96 (0.15), residues: 1221 sheet: 1.05 (0.28), residues: 357 loop : -0.49 (0.21), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 231 HIS 0.004 0.001 HIS C 160 PHE 0.017 0.001 PHE F 31 TYR 0.020 0.001 TYR C 184 ARG 0.014 0.001 ARG I 208 *********************** 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 384 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 284 time to evaluate : 2.661 Fit side-chains REVERT: A 45 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.6583 (mtp85) REVERT: A 163 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7494 (ttt) REVERT: A 185 GLU cc_start: 0.7614 (tt0) cc_final: 0.7380 (tt0) REVERT: A 227 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7276 (mp) REVERT: A 339 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.6939 (p0) REVERT: A 404 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.7074 (tp40) REVERT: B 198 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7750 (ttp80) REVERT: C 130 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7419 (mtt180) REVERT: E 45 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.6652 (mtp85) REVERT: E 145 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7178 (tt0) REVERT: E 227 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.6988 (mp) REVERT: I 45 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.6636 (mtp85) REVERT: I 145 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7297 (tt0) REVERT: I 185 GLU cc_start: 0.7625 (tt0) cc_final: 0.7393 (tt0) REVERT: I 227 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7054 (mp) REVERT: J 241 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7210 (mt-10) REVERT: G 130 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7547 (mtp85) REVERT: G 156 ASP cc_start: 0.6152 (OUTLIER) cc_final: 0.5399 (m-30) REVERT: G 235 PHE cc_start: 0.6691 (OUTLIER) cc_final: 0.6218 (t80) REVERT: K 156 ASP cc_start: 0.6112 (OUTLIER) cc_final: 0.5322 (m-30) outliers start: 100 outliers final: 39 residues processed: 353 average time/residue: 1.3466 time to fit residues: 544.4363 Evaluate side-chains 328 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 271 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 404 GLN 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 198 ARG Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 145 GLN Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 414 MET Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 145 GLN Chi-restraints excluded: chain I residue 207 SER Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 228 VAL 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 69 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 241 GLU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 130 ARG Chi-restraints excluded: chain G residue 156 ASP Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 235 PHE Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 240 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 205 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 210 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 221 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN B 187 ASN ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 ASN G 91 ASN G 155 GLN K 91 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 23142 Z= 0.531 Angle : 0.804 9.092 31314 Z= 0.415 Chirality : 0.052 0.240 3207 Planarity : 0.006 0.046 3732 Dihedral : 20.202 167.081 4176 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.24 % Favored : 94.37 % Rotamer: Outliers : 5.08 % Allowed : 17.47 % Favored : 77.46 % 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: 0.32 (0.17), residues: 2559 helix: 0.80 (0.15), residues: 1212 sheet: 0.75 (0.27), residues: 369 loop : -0.66 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP J 231 HIS 0.012 0.002 HIS C 160 PHE 0.022 0.003 PHE B 31 TYR 0.030 0.003 TYR C 184 ARG 0.012 0.001 ARG K 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 271 time to evaluate : 2.650 Fit side-chains revert: symmetry clash REVERT: A 145 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7228 (tt0) REVERT: A 163 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7794 (ttt) REVERT: A 339 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7066 (p0) REVERT: A 404 GLN cc_start: 0.7377 (OUTLIER) cc_final: 0.7018 (tp40) REVERT: C 115 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.6981 (ptp-170) REVERT: C 130 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7438 (mtt180) REVERT: E 145 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7471 (tt0) REVERT: E 227 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7458 (mp) REVERT: I 145 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7576 (tt0) REVERT: I 167 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6786 (mmp80) REVERT: I 185 GLU cc_start: 0.7746 (tt0) cc_final: 0.7451 (tt0) REVERT: I 227 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7287 (mp) REVERT: F 198 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7989 (ttp80) REVERT: J 241 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7237 (mt-10) REVERT: G 115 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.6962 (ptp-170) REVERT: G 126 GLU cc_start: 0.5654 (OUTLIER) cc_final: 0.5374 (mt-10) REVERT: G 130 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7569 (mtp85) REVERT: G 235 PHE cc_start: 0.7053 (OUTLIER) cc_final: 0.6777 (t80) REVERT: K 130 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7250 (mtt90) outliers start: 111 outliers final: 47 residues processed: 345 average time/residue: 1.3957 time to fit residues: 554.4701 Evaluate side-chains 319 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 254 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 145 GLN Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 296 ARG Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 145 GLN Chi-restraints excluded: chain I residue 167 ARG Chi-restraints excluded: chain I residue 207 SER 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 414 MET Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 241 GLU Chi-restraints excluded: chain J residue 245 GLN Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 126 GLU Chi-restraints excluded: chain G residue 130 ARG Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 235 PHE Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 130 ARG Chi-restraints excluded: chain K residue 240 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 82 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 246 optimal weight: 4.9990 chunk 204 optimal weight: 0.9990 chunk 114 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN B 187 ASN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 ASN G 91 ASN K 91 ASN K 276 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23142 Z= 0.196 Angle : 0.617 8.272 31314 Z= 0.314 Chirality : 0.045 0.205 3207 Planarity : 0.004 0.042 3732 Dihedral : 19.336 161.074 4176 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.30 % Favored : 95.55 % Rotamer: Outliers : 4.07 % Allowed : 18.56 % Favored : 77.37 % 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: 0.56 (0.17), residues: 2559 helix: 0.99 (0.15), residues: 1218 sheet: 0.99 (0.28), residues: 357 loop : -0.56 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 206 HIS 0.005 0.001 HIS C 160 PHE 0.016 0.001 PHE B 31 TYR 0.019 0.001 TYR G 184 ARG 0.007 0.000 ARG K 129 *********************** 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 369 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 280 time to evaluate : 2.427 Fit side-chains revert: symmetry clash REVERT: A 45 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.6484 (mtp85) REVERT: A 145 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7105 (tt0) REVERT: A 185 GLU cc_start: 0.7652 (tt0) cc_final: 0.7371 (tt0) REVERT: A 339 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.6964 (p0) REVERT: E 45 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.6512 (mtp85) REVERT: E 227 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7107 (mp) REVERT: I 167 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6708 (mmp80) REVERT: I 185 GLU cc_start: 0.7642 (tt0) cc_final: 0.7358 (tt0) REVERT: I 227 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7259 (mp) REVERT: F 198 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7865 (ttp80) REVERT: J 241 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7207 (mt-10) outliers start: 89 outliers final: 41 residues processed: 350 average time/residue: 1.2959 time to fit residues: 521.0662 Evaluate side-chains 320 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 270 time to evaluate : 2.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 167 ARG Chi-restraints excluded: chain I residue 207 SER Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 198 ARG Chi-restraints excluded: chain J residue 241 GLU Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 240 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 237 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 140 optimal weight: 0.7980 chunk 180 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 245 optimal weight: 4.9990 chunk 153 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 ASN B 187 ASN ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 ASN G 91 ASN K 91 ASN K 118 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 23142 Z= 0.426 Angle : 0.734 9.014 31314 Z= 0.379 Chirality : 0.049 0.209 3207 Planarity : 0.005 0.047 3732 Dihedral : 19.154 158.026 4172 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.39 % Favored : 94.29 % Rotamer: Outliers : 4.21 % Allowed : 18.47 % Favored : 77.32 % 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: 0.44 (0.17), residues: 2559 helix: 0.95 (0.15), residues: 1215 sheet: 0.76 (0.28), residues: 369 loop : -0.65 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J 231 HIS 0.008 0.002 HIS C 160 PHE 0.023 0.003 PHE G 235 TYR 0.028 0.003 TYR C 184 ARG 0.009 0.001 ARG C 129 *********************** 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 356 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 264 time to evaluate : 2.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7168 (tt0) REVERT: A 185 GLU cc_start: 0.7728 (tt0) cc_final: 0.7418 (tt0) REVERT: A 339 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7028 (p0) REVERT: A 404 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.7039 (tp40) REVERT: C 115 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.6973 (ptp-170) REVERT: C 130 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7434 (mtt180) REVERT: E 145 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7358 (tt0) REVERT: E 227 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7396 (mp) REVERT: E 296 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7569 (ptm-80) REVERT: I 145 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7545 (tt0) REVERT: I 167 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.6762 (mmp80) REVERT: I 185 GLU cc_start: 0.7727 (tt0) cc_final: 0.7420 (tt0) REVERT: I 227 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7354 (mp) REVERT: F 198 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7959 (ttp80) REVERT: J 241 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7206 (mt-10) REVERT: G 115 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.6955 (ptp-170) REVERT: K 130 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7435 (mtt90) outliers start: 92 outliers final: 52 residues processed: 329 average time/residue: 1.3862 time to fit residues: 518.9669 Evaluate side-chains 329 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 262 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain E residue 33 HIS Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 79 GLU Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 145 GLN Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 296 ARG Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 79 GLU Chi-restraints excluded: chain I residue 145 GLN Chi-restraints excluded: chain I residue 167 ARG Chi-restraints excluded: chain I residue 207 SER 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 33 ILE Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 198 ARG Chi-restraints excluded: chain J residue 241 GLU Chi-restraints excluded: chain J residue 245 GLN Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 115 ARG 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 115 ARG Chi-restraints excluded: chain K residue 130 ARG Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 240 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 152 optimal weight: 10.0000 chunk 98 optimal weight: 0.0010 chunk 146 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 156 optimal weight: 5.9990 chunk 167 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 193 optimal weight: 0.0670 overall best weight: 0.5124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN B 187 ASN C 91 ASN C 276 GLN E 176 GLN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 187 ASN J 187 ASN G 91 ASN K 91 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23142 Z= 0.174 Angle : 0.613 8.338 31314 Z= 0.312 Chirality : 0.044 0.179 3207 Planarity : 0.004 0.042 3732 Dihedral : 18.443 152.931 4172 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.38 % Favored : 95.39 % Rotamer: Outliers : 3.20 % Allowed : 19.94 % Favored : 76.86 % 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: 0.70 (0.17), residues: 2559 helix: 1.08 (0.15), residues: 1212 sheet: 1.07 (0.29), residues: 354 loop : -0.45 (0.21), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 202 HIS 0.005 0.001 HIS C 160 PHE 0.014 0.001 PHE B 31 TYR 0.018 0.001 TYR K 184 ARG 0.005 0.000 ARG A 208 *********************** 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 356 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 286 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 GLU cc_start: 0.7627 (tt0) cc_final: 0.7304 (tt0) REVERT: A 227 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7369 (mp) REVERT: A 339 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.6934 (p0) REVERT: E 102 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: I 45 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.6460 (mtp85) REVERT: I 167 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.6752 (mmp80) REVERT: I 185 GLU cc_start: 0.7610 (tt0) cc_final: 0.7322 (tt0) REVERT: I 227 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7254 (mp) REVERT: F 198 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7851 (ttp80) outliers start: 70 outliers final: 39 residues processed: 342 average time/residue: 1.3381 time to fit residues: 525.2294 Evaluate side-chains 322 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 276 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 167 ARG Chi-restraints excluded: chain I residue 207 SER Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 198 ARG Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 115 ARG Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 240 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 223 optimal weight: 7.9990 chunk 235 optimal weight: 1.9990 chunk 214 optimal weight: 0.9980 chunk 229 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 179 optimal weight: 0.0980 chunk 70 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 chunk 216 optimal weight: 5.9990 chunk 228 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN B 187 ASN C 155 GLN ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 ASN G 91 ASN K 91 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23142 Z= 0.220 Angle : 0.640 10.590 31314 Z= 0.327 Chirality : 0.045 0.172 3207 Planarity : 0.004 0.088 3732 Dihedral : 18.141 151.648 4172 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.77 % Favored : 94.96 % Rotamer: Outliers : 2.65 % Allowed : 20.85 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.17), residues: 2559 helix: 1.07 (0.15), residues: 1218 sheet: 1.00 (0.28), residues: 357 loop : -0.39 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 231 HIS 0.005 0.001 HIS C 160 PHE 0.019 0.002 PHE K 248 TYR 0.021 0.002 TYR K 184 ARG 0.020 0.000 ARG A 208 *********************** 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 333 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 275 time to evaluate : 2.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 GLU cc_start: 0.7669 (tt0) cc_final: 0.7341 (tt0) REVERT: A 227 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7416 (mp) REVERT: A 339 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.6946 (p0) REVERT: A 404 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.7072 (tp40) REVERT: E 102 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7846 (mp0) REVERT: E 227 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7264 (mp) REVERT: I 45 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.6527 (mtp85) REVERT: I 167 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6680 (mmp80) REVERT: I 185 GLU cc_start: 0.7666 (tt0) cc_final: 0.7372 (tt0) REVERT: I 227 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7372 (mp) REVERT: F 198 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7850 (ttp80) REVERT: G 163 ILE cc_start: 0.7969 (pp) cc_final: 0.7665 (pp) outliers start: 58 outliers final: 39 residues processed: 318 average time/residue: 1.3166 time to fit residues: 479.9824 Evaluate side-chains 315 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 267 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 404 GLN Chi-restraints excluded: chain A residue 414 MET Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 102 GLU Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 167 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 198 ARG Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 115 ARG Chi-restraints excluded: chain K residue 240 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 150 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 254 optimal weight: 4.9990 chunk 233 optimal weight: 0.7980 chunk 202 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 156 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 ASN K 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23142 Z= 0.265 Angle : 0.663 9.897 31314 Z= 0.340 Chirality : 0.046 0.199 3207 Planarity : 0.005 0.077 3732 Dihedral : 17.992 149.767 4172 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.88 % Favored : 94.88 % Rotamer: Outliers : 2.70 % Allowed : 21.26 % Favored : 76.04 % 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: 0.70 (0.17), residues: 2559 helix: 1.06 (0.15), residues: 1218 sheet: 0.98 (0.28), residues: 357 loop : -0.39 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 231 HIS 0.006 0.001 HIS C 160 PHE 0.019 0.002 PHE K 248 TYR 0.023 0.002 TYR C 184 ARG 0.019 0.001 ARG A 208 ********************** 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 331 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 272 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.6643 (mtp85) REVERT: A 185 GLU cc_start: 0.7695 (tt0) cc_final: 0.7396 (tt0) REVERT: A 227 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7584 (mp) REVERT: A 339 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.6955 (p0) REVERT: C 235 PHE cc_start: 0.6773 (t80) cc_final: 0.6518 (t80) REVERT: E 45 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.6643 (mtp85) REVERT: I 45 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.6732 (mtp85) REVERT: I 167 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.6731 (mmp80) REVERT: I 185 GLU cc_start: 0.7684 (tt0) cc_final: 0.7387 (tt0) REVERT: I 227 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7407 (mp) REVERT: F 198 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7919 (ttp80) REVERT: G 163 ILE cc_start: 0.8028 (pp) cc_final: 0.7743 (pp) outliers start: 59 outliers final: 40 residues processed: 321 average time/residue: 1.3104 time to fit residues: 484.3889 Evaluate side-chains 313 residues out of total 2187 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 265 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain E residue 37 SER Chi-restraints excluded: chain E residue 45 ARG Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 363 ASP Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain I residue 33 HIS Chi-restraints excluded: chain I residue 37 SER Chi-restraints excluded: chain I residue 45 ARG Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 167 ARG Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 309 ASN Chi-restraints excluded: chain I residue 363 ASP Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 198 ARG Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 39 ILE Chi-restraints excluded: chain J residue 59 LEU Chi-restraints excluded: chain J residue 198 ARG Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain K residue 74 TRP Chi-restraints excluded: chain K residue 115 ARG Chi-restraints excluded: chain K residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 160 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 56 optimal weight: 0.6980 chunk 202 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 208 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 ASN K 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.147177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.123548 restraints weight = 32549.772| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.22 r_work: 0.3514 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23142 Z= 0.213 Angle : 0.630 9.407 31314 Z= 0.321 Chirality : 0.045 0.164 3207 Planarity : 0.004 0.076 3732 Dihedral : 17.716 147.949 4172 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.65 % Favored : 95.04 % Rotamer: Outliers : 2.42 % Allowed : 21.44 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.17), residues: 2559 helix: 1.06 (0.15), residues: 1218 sheet: 1.01 (0.29), residues: 357 loop : -0.37 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 237 HIS 0.005 0.001 HIS C 160 PHE 0.017 0.001 PHE C 235 TYR 0.021 0.002 TYR G 184 ARG 0.018 0.001 ARG A 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9457.13 seconds wall clock time: 168 minutes 13.17 seconds (10093.17 seconds total)