Starting phenix.real_space_refine on Fri Mar 6 20:51:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lf1_23297/03_2026/7lf1_23297.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lf1_23297/03_2026/7lf1_23297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lf1_23297/03_2026/7lf1_23297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lf1_23297/03_2026/7lf1_23297.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lf1_23297/03_2026/7lf1_23297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lf1_23297/03_2026/7lf1_23297.map" } resolution = 4.04 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.010 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 5 Type Number sf(0) Gaussians Mn 12 7.51 5 S 120 5.16 5 C 21810 2.51 5 N 5814 2.21 5 O 6762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34518 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2409 Classifications: {'peptide': 317} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 294} Chain: "D" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1713 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1629 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, J, M, N, F, G, K, O, P, H, I, L, Q, R Time building chain proxies: 4.80, per 1000 atoms: 0.14 Number of scatterers: 34518 At special positions: 0 Unit cell: (116.48, 115.44, 231.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 12 24.99 S 120 16.00 O 6762 8.00 N 5814 7.00 C 21810 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 152 " - pdb=" SG CYS D 208 " distance=2.02 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 152 " - pdb=" SG CYS F 208 " distance=2.02 Simple disulfide: pdb=" SG CYS G 152 " - pdb=" SG CYS G 208 " distance=2.02 Simple disulfide: pdb=" SG CYS K 152 " - pdb=" SG CYS K 208 " distance=2.02 Simple disulfide: pdb=" SG CYS O 152 " - pdb=" SG CYS O 208 " distance=2.02 Simple disulfide: pdb=" SG CYS P 152 " - pdb=" SG CYS P 208 " distance=2.02 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.02 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 194 " distance=2.02 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 134 " - pdb=" SG CYS Q 194 " distance=2.02 Simple disulfide: pdb=" SG CYS R 134 " - pdb=" SG CYS R 194 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.60 Conformation dependent library (CDL) restraints added in 1.5 seconds 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8280 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 72 sheets defined 21.9% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 23 through 26 Processing helix chain 'A' and resid 27 through 34 Processing helix chain 'A' and resid 35 through 42 removed outlier: 3.721A pdb=" N GLU A 42 " --> pdb=" O GLU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 90 removed outlier: 3.554A pdb=" N ASN A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 115 removed outlier: 4.286A pdb=" N GLY A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 removed outlier: 3.890A pdb=" N LEU A 148 " --> pdb=" O PRO A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 153 Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 183 through 194 Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 207 through 220 Processing helix chain 'A' and resid 253 through 268 Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 285 through 304 removed outlier: 3.501A pdb=" N VAL A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 202 removed outlier: 3.816A pdb=" N GLY D 202 " --> pdb=" O SER D 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.823A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 127 Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'F' and resid 198 through 202 removed outlier: 3.816A pdb=" N GLY F 202 " --> pdb=" O SER F 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 202 removed outlier: 3.817A pdb=" N GLY G 202 " --> pdb=" O SER G 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.822A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 127 Processing helix chain 'H' and resid 183 through 188 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.822A pdb=" N PHE I 83 " --> pdb=" O PRO I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 127 Processing helix chain 'I' and resid 183 through 188 Processing helix chain 'K' and resid 198 through 202 removed outlier: 3.816A pdb=" N GLY K 202 " --> pdb=" O SER K 199 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.822A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 188 Processing helix chain 'O' and resid 198 through 202 removed outlier: 3.816A pdb=" N GLY O 202 " --> pdb=" O SER O 199 " (cutoff:3.500A) Processing helix chain 'P' and resid 198 through 202 removed outlier: 3.816A pdb=" N GLY P 202 " --> pdb=" O SER P 199 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 83 removed outlier: 3.822A pdb=" N PHE Q 83 " --> pdb=" O PRO Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 121 through 127 Processing helix chain 'Q' and resid 183 through 188 Processing helix chain 'R' and resid 79 through 83 removed outlier: 3.822A pdb=" N PHE R 83 " --> pdb=" O PRO R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 127 Processing helix chain 'R' and resid 183 through 188 Processing helix chain 'B' and resid 23 through 26 Processing helix chain 'B' and resid 27 through 34 Processing helix chain 'B' and resid 35 through 42 removed outlier: 3.721A pdb=" N GLU B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 90 removed outlier: 3.554A pdb=" N ASN B 90 " --> pdb=" O GLU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 115 removed outlier: 4.286A pdb=" N GLY B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 149 removed outlier: 3.890A pdb=" N LEU B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 153 Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 183 through 194 Processing helix chain 'B' and resid 200 through 207 Processing helix chain 'B' and resid 207 through 220 Processing helix chain 'B' and resid 253 through 268 Processing helix chain 'B' and resid 279 through 283 Processing helix chain 'B' and resid 285 through 304 removed outlier: 3.501A pdb=" N VAL B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 26 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 35 through 42 removed outlier: 3.721A pdb=" N GLU C 42 " --> pdb=" O GLU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 90 removed outlier: 3.554A pdb=" N ASN C 90 " --> pdb=" O GLU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 115 removed outlier: 4.286A pdb=" N GLY C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL C 114 " --> pdb=" O GLY C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 149 removed outlier: 3.890A pdb=" N LEU C 148 " --> pdb=" O PRO C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 153 Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 183 through 194 Processing helix chain 'C' and resid 200 through 207 Processing helix chain 'C' and resid 207 through 220 Processing helix chain 'C' and resid 253 through 268 Processing helix chain 'C' and resid 279 through 283 Processing helix chain 'C' and resid 285 through 304 removed outlier: 3.501A pdb=" N VAL C 289 " --> pdb=" O THR C 285 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 26 Processing helix chain 'J' and resid 27 through 34 Processing helix chain 'J' and resid 35 through 42 removed outlier: 3.720A pdb=" N GLU J 42 " --> pdb=" O GLU J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 90 removed outlier: 3.555A pdb=" N ASN J 90 " --> pdb=" O GLU J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 115 removed outlier: 4.286A pdb=" N GLY J 106 " --> pdb=" O SER J 102 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL J 114 " --> pdb=" O GLY J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 149 removed outlier: 3.890A pdb=" N LEU J 148 " --> pdb=" O PRO J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 153 Processing helix chain 'J' and resid 170 through 172 No H-bonds generated for 'chain 'J' and resid 170 through 172' Processing helix chain 'J' and resid 183 through 194 Processing helix chain 'J' and resid 200 through 207 Processing helix chain 'J' and resid 207 through 220 Processing helix chain 'J' and resid 253 through 268 Processing helix chain 'J' and resid 279 through 283 Processing helix chain 'J' and resid 285 through 304 removed outlier: 3.501A pdb=" N VAL J 289 " --> pdb=" O THR J 285 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 26 Processing helix chain 'M' and resid 27 through 34 Processing helix chain 'M' and resid 35 through 42 removed outlier: 3.721A pdb=" N GLU M 42 " --> pdb=" O GLU M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 90 removed outlier: 3.554A pdb=" N ASN M 90 " --> pdb=" O GLU M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 102 through 115 removed outlier: 4.286A pdb=" N GLY M 106 " --> pdb=" O SER M 102 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL M 114 " --> pdb=" O GLY M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 149 removed outlier: 3.891A pdb=" N LEU M 148 " --> pdb=" O PRO M 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 150 through 153 Processing helix chain 'M' and resid 170 through 172 No H-bonds generated for 'chain 'M' and resid 170 through 172' Processing helix chain 'M' and resid 183 through 194 Processing helix chain 'M' and resid 200 through 207 Processing helix chain 'M' and resid 207 through 220 Processing helix chain 'M' and resid 253 through 268 Processing helix chain 'M' and resid 279 through 283 Processing helix chain 'M' and resid 285 through 304 removed outlier: 3.501A pdb=" N VAL M 289 " --> pdb=" O THR M 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 26 Processing helix chain 'N' and resid 27 through 34 Processing helix chain 'N' and resid 35 through 42 removed outlier: 3.721A pdb=" N GLU N 42 " --> pdb=" O GLU N 38 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 90 removed outlier: 3.554A pdb=" N ASN N 90 " --> pdb=" O GLU N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 102 through 115 removed outlier: 4.286A pdb=" N GLY N 106 " --> pdb=" O SER N 102 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL N 114 " --> pdb=" O GLY N 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 149 removed outlier: 3.890A pdb=" N LEU N 148 " --> pdb=" O PRO N 144 " (cutoff:3.500A) Processing helix chain 'N' and resid 150 through 153 Processing helix chain 'N' and resid 170 through 172 No H-bonds generated for 'chain 'N' and resid 170 through 172' Processing helix chain 'N' and resid 183 through 194 Processing helix chain 'N' and resid 200 through 207 Processing helix chain 'N' and resid 207 through 220 Processing helix chain 'N' and resid 253 through 268 Processing helix chain 'N' and resid 279 through 283 Processing helix chain 'N' and resid 285 through 304 removed outlier: 3.502A pdb=" N VAL N 289 " --> pdb=" O THR N 285 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 52 removed outlier: 6.356A pdb=" N GLY A 12 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP A 52 " --> pdb=" O GLY A 12 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N THR A 7 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU A 95 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N GLY A 9 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU A 97 " --> pdb=" O GLY A 9 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE A 11 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 94 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE A 227 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU A 273 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU A 229 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE A 275 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE A 231 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY A 119 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER A 230 " --> pdb=" O GLY A 119 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ILE A 121 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP A 232 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL A 123 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL A 120 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE A 177 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP A 122 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU A 179 " --> pdb=" O TRP A 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'D' and resid 45 through 50 removed outlier: 6.479A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N SER D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 121 " --> pdb=" O ALA D 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 69 through 72 removed outlier: 3.782A pdb=" N THR D 69 " --> pdb=" O GLU D 82 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 150 through 151 removed outlier: 6.744A pdb=" N SER D 189 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP D 156 " --> pdb=" O SER D 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 150 through 151 removed outlier: 5.160A pdb=" N SER D 192 " --> pdb=" O PRO D 179 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N VAL D 194 " --> pdb=" O THR D 177 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N THR D 177 " --> pdb=" O VAL D 194 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 209 through 212 Processing sheet with id=AA8, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.456A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 46 through 48 removed outlier: 6.301A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 117 through 118 removed outlier: 3.509A pdb=" N SER E 177 " --> pdb=" O CYS E 134 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 154 through 155 removed outlier: 3.724A pdb=" N TRP E 148 " --> pdb=" O GLN E 155 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'F' and resid 45 through 50 removed outlier: 6.480A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE F 34 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL F 121 " --> pdb=" O ALA F 92 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 69 through 72 removed outlier: 3.781A pdb=" N THR F 69 " --> pdb=" O GLU F 82 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 150 through 151 removed outlier: 6.744A pdb=" N SER F 189 " --> pdb=" O ASP F 156 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP F 156 " --> pdb=" O SER F 189 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 150 through 151 removed outlier: 5.161A pdb=" N SER F 192 " --> pdb=" O PRO F 179 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N VAL F 194 " --> pdb=" O THR F 177 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N THR F 177 " --> pdb=" O VAL F 194 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 209 through 212 Processing sheet with id=AC1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'G' and resid 45 through 50 removed outlier: 6.480A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE G 34 " --> pdb=" O SER G 50 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL G 121 " --> pdb=" O ALA G 92 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 69 through 72 removed outlier: 3.782A pdb=" N THR G 69 " --> pdb=" O GLU G 82 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 150 through 151 removed outlier: 6.744A pdb=" N SER G 189 " --> pdb=" O ASP G 156 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP G 156 " --> pdb=" O SER G 189 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 150 through 151 removed outlier: 5.161A pdb=" N SER G 192 " --> pdb=" O PRO G 179 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N VAL G 194 " --> pdb=" O THR G 177 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N THR G 177 " --> pdb=" O VAL G 194 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 209 through 212 Processing sheet with id=AC7, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AC8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.456A pdb=" N LEU H 11 " --> pdb=" O GLU H 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'H' and resid 46 through 48 removed outlier: 6.301A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 117 through 118 removed outlier: 3.509A pdb=" N SER H 177 " --> pdb=" O CYS H 134 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 154 through 155 removed outlier: 3.724A pdb=" N TRP H 148 " --> pdb=" O GLN H 155 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AD4, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.457A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'I' and resid 46 through 48 removed outlier: 6.299A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 117 through 118 removed outlier: 3.509A pdb=" N SER I 177 " --> pdb=" O CYS I 134 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 154 through 155 removed outlier: 3.724A pdb=" N TRP I 148 " --> pdb=" O GLN I 155 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AD9, first strand: chain 'K' and resid 45 through 50 removed outlier: 6.479A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N SER K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE K 34 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL K 121 " --> pdb=" O ALA K 92 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 69 through 72 removed outlier: 3.782A pdb=" N THR K 69 " --> pdb=" O GLU K 82 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 150 through 151 removed outlier: 6.744A pdb=" N SER K 189 " --> pdb=" O ASP K 156 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP K 156 " --> pdb=" O SER K 189 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 150 through 151 removed outlier: 5.160A pdb=" N SER K 192 " --> pdb=" O PRO K 179 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N VAL K 194 " --> pdb=" O THR K 177 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N THR K 177 " --> pdb=" O VAL K 194 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 209 through 212 Processing sheet with id=AE5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AE6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.456A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'L' and resid 46 through 48 removed outlier: 6.300A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 117 through 118 removed outlier: 3.509A pdb=" N SER L 177 " --> pdb=" O CYS L 134 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 154 through 155 removed outlier: 3.724A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'O' and resid 45 through 50 removed outlier: 6.480A pdb=" N TRP O 36 " --> pdb=" O MET O 48 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N SER O 50 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE O 34 " --> pdb=" O SER O 50 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL O 121 " --> pdb=" O ALA O 92 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 69 through 72 removed outlier: 3.782A pdb=" N THR O 69 " --> pdb=" O GLU O 82 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 150 through 151 removed outlier: 6.744A pdb=" N SER O 189 " --> pdb=" O ASP O 156 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP O 156 " --> pdb=" O SER O 189 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 150 through 151 removed outlier: 5.161A pdb=" N SER O 192 " --> pdb=" O PRO O 179 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N VAL O 194 " --> pdb=" O THR O 177 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N THR O 177 " --> pdb=" O VAL O 194 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'O' and resid 209 through 212 Processing sheet with id=AF7, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AF8, first strand: chain 'P' and resid 45 through 50 removed outlier: 6.480A pdb=" N TRP P 36 " --> pdb=" O MET P 48 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N SER P 50 " --> pdb=" O ILE P 34 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE P 34 " --> pdb=" O SER P 50 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL P 121 " --> pdb=" O ALA P 92 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'P' and resid 69 through 72 removed outlier: 3.781A pdb=" N THR P 69 " --> pdb=" O GLU P 82 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'P' and resid 150 through 151 removed outlier: 6.744A pdb=" N SER P 189 " --> pdb=" O ASP P 156 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP P 156 " --> pdb=" O SER P 189 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'P' and resid 150 through 151 removed outlier: 5.161A pdb=" N SER P 192 " --> pdb=" O PRO P 179 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N VAL P 194 " --> pdb=" O THR P 177 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N THR P 177 " --> pdb=" O VAL P 194 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'P' and resid 209 through 212 Processing sheet with id=AG4, first strand: chain 'Q' and resid 4 through 6 Processing sheet with id=AG5, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.456A pdb=" N LEU Q 11 " --> pdb=" O GLU Q 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'Q' and resid 46 through 48 removed outlier: 6.300A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Q' and resid 117 through 118 removed outlier: 3.509A pdb=" N SER Q 177 " --> pdb=" O CYS Q 134 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 154 through 155 removed outlier: 3.724A pdb=" N TRP Q 148 " --> pdb=" O GLN Q 155 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'R' and resid 4 through 6 Processing sheet with id=AH1, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.456A pdb=" N LEU R 11 " --> pdb=" O GLU R 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'R' and resid 46 through 48 removed outlier: 6.300A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'R' and resid 117 through 118 removed outlier: 3.509A pdb=" N SER R 177 " --> pdb=" O CYS R 134 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'R' and resid 154 through 155 removed outlier: 3.723A pdb=" N TRP R 148 " --> pdb=" O GLN R 155 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.357A pdb=" N GLY B 12 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP B 52 " --> pdb=" O GLY B 12 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N THR B 7 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU B 95 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N GLY B 9 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU B 97 " --> pdb=" O GLY B 9 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE B 11 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 94 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE B 227 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU B 273 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU B 229 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE B 275 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE B 231 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY B 119 " --> pdb=" O HIS B 228 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N SER B 230 " --> pdb=" O GLY B 119 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ILE B 121 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP B 232 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL B 123 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL B 120 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE B 177 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TRP B 122 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU B 179 " --> pdb=" O TRP B 122 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 46 through 52 removed outlier: 6.356A pdb=" N GLY C 12 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP C 52 " --> pdb=" O GLY C 12 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR C 7 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU C 95 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N GLY C 9 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU C 97 " --> pdb=" O GLY C 9 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE C 11 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER C 94 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE C 227 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU C 273 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU C 229 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE C 275 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE C 231 " --> pdb=" O ILE C 275 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY C 119 " --> pdb=" O HIS C 228 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER C 230 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ILE C 121 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP C 232 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL C 123 " --> pdb=" O ASP C 232 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL C 120 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE C 177 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP C 122 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU C 179 " --> pdb=" O TRP C 122 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 46 through 52 removed outlier: 6.357A pdb=" N GLY J 12 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP J 52 " --> pdb=" O GLY J 12 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR J 7 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU J 95 " --> pdb=" O THR J 7 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N GLY J 9 " --> pdb=" O LEU J 95 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU J 97 " --> pdb=" O GLY J 9 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE J 11 " --> pdb=" O LEU J 97 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER J 94 " --> pdb=" O SER J 271 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE J 227 " --> pdb=" O SER J 271 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU J 273 " --> pdb=" O ILE J 227 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU J 229 " --> pdb=" O LEU J 273 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE J 275 " --> pdb=" O LEU J 229 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N PHE J 231 " --> pdb=" O ILE J 275 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY J 119 " --> pdb=" O HIS J 228 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER J 230 " --> pdb=" O GLY J 119 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ILE J 121 " --> pdb=" O SER J 230 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP J 232 " --> pdb=" O ILE J 121 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL J 123 " --> pdb=" O ASP J 232 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL J 120 " --> pdb=" O VAL J 175 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE J 177 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP J 122 " --> pdb=" O ILE J 177 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU J 179 " --> pdb=" O TRP J 122 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'M' and resid 46 through 52 removed outlier: 6.357A pdb=" N GLY M 12 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP M 52 " --> pdb=" O GLY M 12 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR M 7 " --> pdb=" O ILE M 93 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU M 95 " --> pdb=" O THR M 7 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N GLY M 9 " --> pdb=" O LEU M 95 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU M 97 " --> pdb=" O GLY M 9 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE M 11 " --> pdb=" O LEU M 97 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER M 94 " --> pdb=" O SER M 271 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE M 227 " --> pdb=" O SER M 271 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU M 273 " --> pdb=" O ILE M 227 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU M 229 " --> pdb=" O LEU M 273 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE M 275 " --> pdb=" O LEU M 229 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N PHE M 231 " --> pdb=" O ILE M 275 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLY M 119 " --> pdb=" O HIS M 228 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER M 230 " --> pdb=" O GLY M 119 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ILE M 121 " --> pdb=" O SER M 230 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP M 232 " --> pdb=" O ILE M 121 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL M 123 " --> pdb=" O ASP M 232 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL M 120 " --> pdb=" O VAL M 175 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE M 177 " --> pdb=" O VAL M 120 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP M 122 " --> pdb=" O ILE M 177 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU M 179 " --> pdb=" O TRP M 122 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'N' and resid 46 through 52 removed outlier: 6.356A pdb=" N GLY N 12 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASP N 52 " --> pdb=" O GLY N 12 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N THR N 7 " --> pdb=" O ILE N 93 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU N 95 " --> pdb=" O THR N 7 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N GLY N 9 " --> pdb=" O LEU N 95 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU N 97 " --> pdb=" O GLY N 9 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE N 11 " --> pdb=" O LEU N 97 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER N 94 " --> pdb=" O SER N 271 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE N 227 " --> pdb=" O SER N 271 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU N 273 " --> pdb=" O ILE N 227 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU N 229 " --> pdb=" O LEU N 273 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE N 275 " --> pdb=" O LEU N 229 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N PHE N 231 " --> pdb=" O ILE N 275 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY N 119 " --> pdb=" O HIS N 228 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER N 230 " --> pdb=" O GLY N 119 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ILE N 121 " --> pdb=" O SER N 230 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ASP N 232 " --> pdb=" O ILE N 121 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL N 123 " --> pdb=" O ASP N 232 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL N 120 " --> pdb=" O VAL N 175 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILE N 177 " --> pdb=" O VAL N 120 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP N 122 " --> pdb=" O ILE N 177 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU N 179 " --> pdb=" O TRP N 122 " (cutoff:3.500A) 1002 hydrogen bonds defined for protein. 2718 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: 5.91 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11050 1.34 - 1.46: 7306 1.46 - 1.58: 16756 1.58 - 1.69: 0 1.69 - 1.81: 162 Bond restraints: 35274 Sorted by residual: bond pdb=" C LYS G 13 " pdb=" N PRO G 14 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.66e+00 bond pdb=" C LYS P 13 " pdb=" N PRO P 14 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.60e+00 bond pdb=" C LYS D 13 " pdb=" N PRO D 14 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.54e+00 bond pdb=" C LYS F 13 " pdb=" N PRO F 14 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.52e+00 bond pdb=" C LYS K 13 " pdb=" N PRO K 14 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.48e+00 ... (remaining 35269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 46616 2.77 - 5.54: 1073 5.54 - 8.31: 191 8.31 - 11.08: 54 11.08 - 13.85: 6 Bond angle restraints: 47940 Sorted by residual: angle pdb=" C PHE P 112 " pdb=" N ASP P 113 " pdb=" CA ASP P 113 " ideal model delta sigma weight residual 123.21 113.64 9.57 1.19e+00 7.06e-01 6.47e+01 angle pdb=" C PHE G 112 " pdb=" N ASP G 113 " pdb=" CA ASP G 113 " ideal model delta sigma weight residual 123.21 113.65 9.56 1.19e+00 7.06e-01 6.45e+01 angle pdb=" C PHE O 112 " pdb=" N ASP O 113 " pdb=" CA ASP O 113 " ideal model delta sigma weight residual 123.21 113.68 9.53 1.19e+00 7.06e-01 6.42e+01 angle pdb=" C PHE K 112 " pdb=" N ASP K 113 " pdb=" CA ASP K 113 " ideal model delta sigma weight residual 123.21 113.68 9.53 1.19e+00 7.06e-01 6.41e+01 angle pdb=" C PHE F 112 " pdb=" N ASP F 113 " pdb=" CA ASP F 113 " ideal model delta sigma weight residual 123.21 113.71 9.50 1.19e+00 7.06e-01 6.37e+01 ... (remaining 47935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.91: 19332 11.91 - 23.83: 1392 23.83 - 35.74: 354 35.74 - 47.65: 90 47.65 - 59.57: 12 Dihedral angle restraints: 21180 sinusoidal: 8190 harmonic: 12990 Sorted by residual: dihedral pdb=" CA PRO P 114 " pdb=" C PRO P 114 " pdb=" N TRP P 115 " pdb=" CA TRP P 115 " ideal model delta harmonic sigma weight residual 180.00 -134.66 -45.34 0 5.00e+00 4.00e-02 8.22e+01 dihedral pdb=" CA PRO F 114 " pdb=" C PRO F 114 " pdb=" N TRP F 115 " pdb=" CA TRP F 115 " ideal model delta harmonic sigma weight residual 180.00 -134.68 -45.32 0 5.00e+00 4.00e-02 8.22e+01 dihedral pdb=" CA PRO D 114 " pdb=" C PRO D 114 " pdb=" N TRP D 115 " pdb=" CA TRP D 115 " ideal model delta harmonic sigma weight residual 180.00 -134.69 -45.31 0 5.00e+00 4.00e-02 8.21e+01 ... (remaining 21177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3940 0.053 - 0.105: 1116 0.105 - 0.158: 314 0.158 - 0.211: 78 0.211 - 0.263: 6 Chirality restraints: 5454 Sorted by residual: chirality pdb=" CB ILE L 48 " pdb=" CA ILE L 48 " pdb=" CG1 ILE L 48 " pdb=" CG2 ILE L 48 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB ILE Q 48 " pdb=" CA ILE Q 48 " pdb=" CG1 ILE Q 48 " pdb=" CG2 ILE Q 48 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB ILE I 48 " pdb=" CA ILE I 48 " pdb=" CG1 ILE I 48 " pdb=" CG2 ILE I 48 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 5451 not shown) Planarity restraints: 6144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 13 " 0.068 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO D 14 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO D 14 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO D 14 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS G 13 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO G 14 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO G 14 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO G 14 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS K 13 " 0.068 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO K 14 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO K 14 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO K 14 " 0.058 5.00e-02 4.00e+02 ... (remaining 6141 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 54 2.25 - 2.92: 14748 2.92 - 3.58: 52644 3.58 - 4.24: 90343 4.24 - 4.90: 144355 Nonbonded interactions: 302144 Sorted by model distance: nonbonded pdb=" ND1 HIS M 126 " pdb="MN MN M1002 " model vdw 1.592 2.400 nonbonded pdb=" ND1 HIS J 126 " pdb="MN MN J1002 " model vdw 1.592 2.400 nonbonded pdb=" ND1 HIS C 126 " pdb="MN MN C1002 " model vdw 1.592 2.400 nonbonded pdb=" ND1 HIS A 126 " pdb="MN MN A1002 " model vdw 1.593 2.400 nonbonded pdb=" ND1 HIS B 126 " pdb="MN MN B1002 " model vdw 1.593 2.400 ... (remaining 302139 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'J' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'L' selection = chain 'Q' selection = chain 'R' } 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 group one per residue 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: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 25.920 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 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 : 0.006 0.066 35298 Z= 0.301 Angle : 1.075 13.848 47988 Z= 0.582 Chirality : 0.055 0.263 5454 Planarity : 0.009 0.104 6144 Dihedral : 9.387 59.568 12828 Min Nonbonded Distance : 1.592 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.40 % Allowed : 12.88 % Favored : 86.72 % Rotamer: Outliers : 0.16 % Allowed : 2.51 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.57 % Twisted Proline : 2.17 % Twisted General : 1.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.16 (0.11), residues: 4488 helix: -1.83 (0.14), residues: 792 sheet: -3.35 (0.12), residues: 1302 loop : -2.73 (0.12), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 180 TYR 0.032 0.003 TYR R 49 PHE 0.048 0.004 PHE O 178 TRP 0.023 0.004 TRP P 47 HIS 0.018 0.004 HIS E 91 Details of bonding type rmsd covalent geometry : bond 0.00641 (35274) covalent geometry : angle 1.07345 (47940) SS BOND : bond 0.00589 ( 24) SS BOND : angle 2.05166 ( 48) hydrogen bonds : bond 0.20857 ( 990) hydrogen bonds : angle 9.02024 ( 2718) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 680 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.6879 (p0) cc_final: 0.6349 (p0) REVERT: A 127 THR cc_start: 0.8662 (p) cc_final: 0.7985 (p) REVERT: A 176 TYR cc_start: 0.7851 (m-80) cc_final: 0.7379 (m-80) REVERT: A 254 TYR cc_start: 0.9080 (t80) cc_final: 0.8613 (t80) REVERT: A 274 ASP cc_start: 0.6846 (m-30) cc_final: 0.6299 (t0) REVERT: A 277 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7090 (mt-10) REVERT: A 279 ASN cc_start: 0.8416 (t0) cc_final: 0.8171 (t0) REVERT: F 206 TYR cc_start: 0.6688 (m-80) cc_final: 0.6465 (m-80) REVERT: G 21 SER cc_start: 0.8358 (m) cc_final: 0.8136 (p) REVERT: G 145 GLU cc_start: 0.6642 (mt-10) cc_final: 0.6252 (tm-30) REVERT: K 45 LEU cc_start: 0.3893 (mp) cc_final: 0.2745 (mp) REVERT: K 90 ASP cc_start: 0.6628 (m-30) cc_final: 0.5915 (m-30) REVERT: K 211 ASP cc_start: 0.8327 (m-30) cc_final: 0.7932 (t0) REVERT: L 35 TRP cc_start: 0.7849 (m100) cc_final: 0.7002 (m100) REVERT: L 47 LEU cc_start: 0.8993 (mt) cc_final: 0.8724 (mt) REVERT: O 37 VAL cc_start: 0.9206 (OUTLIER) cc_final: 0.8854 (p) REVERT: O 90 ASP cc_start: 0.5867 (m-30) cc_final: 0.5173 (m-30) REVERT: O 121 VAL cc_start: 0.7523 (t) cc_final: 0.6347 (t) REVERT: O 211 ASP cc_start: 0.8170 (m-30) cc_final: 0.7679 (t0) REVERT: P 36 TRP cc_start: 0.7766 (m100) cc_final: 0.6847 (m100) REVERT: P 89 ASP cc_start: 0.7538 (p0) cc_final: 0.7274 (p0) REVERT: P 112 PHE cc_start: 0.6773 (m-80) cc_final: 0.6298 (m-80) REVERT: P 211 ASP cc_start: 0.8740 (m-30) cc_final: 0.8485 (t0) REVERT: Q 32 TYR cc_start: 0.6993 (m-10) cc_final: 0.5977 (m-80) REVERT: Q 35 TRP cc_start: 0.7582 (m100) cc_final: 0.6040 (m100) REVERT: Q 36 TYR cc_start: 0.7769 (m-80) cc_final: 0.6413 (m-80) REVERT: Q 48 ILE cc_start: 0.8527 (mt) cc_final: 0.8322 (tp) REVERT: Q 87 TYR cc_start: 0.9052 (m-80) cc_final: 0.8679 (m-80) REVERT: R 32 TYR cc_start: 0.7276 (m-10) cc_final: 0.6845 (m-80) REVERT: R 35 TRP cc_start: 0.7574 (m100) cc_final: 0.6502 (m100) REVERT: R 36 TYR cc_start: 0.7954 (m-80) cc_final: 0.7652 (m-80) REVERT: R 47 LEU cc_start: 0.8771 (mt) cc_final: 0.8275 (mt) REVERT: B 100 ASP cc_start: 0.6464 (p0) cc_final: 0.5962 (p0) REVERT: B 127 THR cc_start: 0.8719 (p) cc_final: 0.7948 (p) REVERT: B 176 TYR cc_start: 0.7795 (m-80) cc_final: 0.7197 (m-80) REVERT: B 200 MET cc_start: 0.7900 (mmm) cc_final: 0.7660 (mmt) REVERT: B 274 ASP cc_start: 0.7119 (m-30) cc_final: 0.6583 (t0) REVERT: B 277 GLU cc_start: 0.8672 (mm-30) cc_final: 0.7183 (mt-10) REVERT: B 279 ASN cc_start: 0.8627 (t0) cc_final: 0.8307 (t0) REVERT: C 50 TYR cc_start: 0.7724 (m-80) cc_final: 0.7373 (m-10) REVERT: C 103 LEU cc_start: 0.9096 (mt) cc_final: 0.8847 (mt) REVERT: C 200 MET cc_start: 0.7802 (mmm) cc_final: 0.7037 (tpp) REVERT: C 277 GLU cc_start: 0.8443 (mm-30) cc_final: 0.7173 (mt-10) REVERT: C 279 ASN cc_start: 0.8278 (t0) cc_final: 0.7917 (t0) REVERT: J 108 ILE cc_start: 0.7597 (mt) cc_final: 0.7249 (mt) REVERT: N 108 ILE cc_start: 0.7683 (mt) cc_final: 0.7264 (mt) outliers start: 6 outliers final: 0 residues processed: 684 average time/residue: 0.2352 time to fit residues: 249.9511 Evaluate side-chains 311 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 310 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 30.0000 chunk 388 optimal weight: 0.4980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 50.0000 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 10.0000 chunk 424 optimal weight: 9.9990 overall best weight: 5.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 HIS A 126 HIS ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN D 110 ASN ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 GLN F 39 GLN F 110 ASN ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN G 39 GLN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 110 ASN K 183 GLN L 160 GLN L 189 HIS ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 110 ASN O 183 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 110 ASN P 183 GLN ** Q 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS B 126 HIS ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN B 319 ASN ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS C 126 HIS ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN ** J 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN J 319 ASN ** M 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 ASN M 319 ASN N 90 ASN N 319 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.116621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.088834 restraints weight = 155997.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.085768 restraints weight = 87050.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.086714 restraints weight = 64264.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.086884 restraints weight = 48535.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.086886 restraints weight = 44020.270| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 35298 Z= 0.326 Angle : 0.875 11.358 47988 Z= 0.454 Chirality : 0.050 0.196 5454 Planarity : 0.008 0.099 6144 Dihedral : 7.504 39.265 4878 Min Nonbonded Distance : 1.361 Molprobity Statistics. All-atom Clashscore : 21.93 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.54 % Favored : 88.28 % Rotamer: Outliers : 0.21 % Allowed : 2.12 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.57 % Twisted Proline : 2.17 % Twisted General : 0.54 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.46 (0.12), residues: 4488 helix: -0.89 (0.16), residues: 834 sheet: -2.96 (0.13), residues: 1224 loop : -2.44 (0.12), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 105 TYR 0.041 0.003 TYR K 102 PHE 0.033 0.003 PHE B 64 TRP 0.017 0.003 TRP O 47 HIS 0.012 0.002 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00714 (35274) covalent geometry : angle 0.87471 (47940) SS BOND : bond 0.00907 ( 24) SS BOND : angle 1.14370 ( 48) hydrogen bonds : bond 0.03997 ( 990) hydrogen bonds : angle 7.00440 ( 2718) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 405 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ASP cc_start: 0.8779 (t0) cc_final: 0.8517 (t0) REVERT: A 277 GLU cc_start: 0.8628 (mm-30) cc_final: 0.7789 (mt-10) REVERT: A 279 ASN cc_start: 0.9069 (t0) cc_final: 0.8482 (t0) REVERT: E 70 ASP cc_start: 0.7505 (p0) cc_final: 0.7013 (p0) REVERT: F 81 MET cc_start: 0.7982 (tmm) cc_final: 0.7729 (tmm) REVERT: F 206 TYR cc_start: 0.6985 (m-80) cc_final: 0.6749 (m-80) REVERT: G 145 GLU cc_start: 0.6889 (mt-10) cc_final: 0.6268 (tm-30) REVERT: H 49 TYR cc_start: 0.7182 (OUTLIER) cc_final: 0.6806 (p90) REVERT: I 49 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.6812 (p90) REVERT: K 47 TRP cc_start: 0.7719 (t60) cc_final: 0.7395 (t60) REVERT: K 90 ASP cc_start: 0.8433 (m-30) cc_final: 0.8032 (m-30) REVERT: K 113 ASP cc_start: 0.8112 (p0) cc_final: 0.7287 (p0) REVERT: K 211 ASP cc_start: 0.7988 (m-30) cc_final: 0.7096 (t0) REVERT: L 35 TRP cc_start: 0.6322 (m100) cc_final: 0.5591 (m100) REVERT: L 71 PHE cc_start: 0.8599 (m-80) cc_final: 0.8219 (m-80) REVERT: L 72 THR cc_start: 0.8296 (p) cc_final: 0.8024 (t) REVERT: L 82 ASP cc_start: 0.7420 (m-30) cc_final: 0.6900 (m-30) REVERT: O 48 MET cc_start: 0.9168 (ptp) cc_final: 0.8801 (ptt) REVERT: O 89 ASP cc_start: 0.8977 (p0) cc_final: 0.8150 (p0) REVERT: O 90 ASP cc_start: 0.8331 (m-30) cc_final: 0.6683 (m-30) REVERT: O 211 ASP cc_start: 0.7685 (m-30) cc_final: 0.6958 (t0) REVERT: P 36 TRP cc_start: 0.7923 (m100) cc_final: 0.7638 (m100) REVERT: P 89 ASP cc_start: 0.7913 (p0) cc_final: 0.7392 (p0) REVERT: P 211 ASP cc_start: 0.8231 (m-30) cc_final: 0.7774 (t0) REVERT: Q 32 TYR cc_start: 0.8125 (m-10) cc_final: 0.7749 (m-10) REVERT: Q 35 TRP cc_start: 0.6496 (m100) cc_final: 0.5983 (m100) REVERT: Q 36 TYR cc_start: 0.8347 (m-80) cc_final: 0.7802 (m-80) REVERT: Q 48 ILE cc_start: 0.9065 (mt) cc_final: 0.8817 (pt) REVERT: Q 71 PHE cc_start: 0.8756 (m-80) cc_final: 0.8170 (m-80) REVERT: Q 82 ASP cc_start: 0.7832 (m-30) cc_final: 0.7371 (m-30) REVERT: Q 86 TYR cc_start: 0.9013 (m-10) cc_final: 0.8786 (m-10) REVERT: Q 126 LYS cc_start: 0.7904 (pptt) cc_final: 0.7667 (tmtt) REVERT: R 35 TRP cc_start: 0.5830 (m100) cc_final: 0.5255 (m100) REVERT: R 36 TYR cc_start: 0.8259 (m-80) cc_final: 0.7949 (m-80) REVERT: R 70 ASP cc_start: 0.8787 (t0) cc_final: 0.8586 (t0) REVERT: R 71 PHE cc_start: 0.8404 (m-80) cc_final: 0.7878 (m-80) REVERT: R 72 THR cc_start: 0.8141 (p) cc_final: 0.7836 (t) REVERT: R 82 ASP cc_start: 0.7342 (m-30) cc_final: 0.6884 (m-30) REVERT: R 86 TYR cc_start: 0.9206 (m-10) cc_final: 0.8996 (m-10) REVERT: R 87 TYR cc_start: 0.8643 (m-80) cc_final: 0.8415 (m-80) REVERT: B 277 GLU cc_start: 0.8670 (mm-30) cc_final: 0.7633 (mt-10) REVERT: B 279 ASN cc_start: 0.9121 (t0) cc_final: 0.8521 (t0) REVERT: C 200 MET cc_start: 0.9021 (mmm) cc_final: 0.8814 (tpp) REVERT: C 277 GLU cc_start: 0.8584 (mm-30) cc_final: 0.7876 (mt-10) REVERT: C 279 ASN cc_start: 0.8920 (t0) cc_final: 0.8305 (t0) REVERT: J 15 PHE cc_start: 0.8659 (t80) cc_final: 0.8305 (t80) REVERT: J 43 GLN cc_start: 0.8723 (pp30) cc_final: 0.8308 (pp30) REVERT: J 95 LEU cc_start: 0.8571 (tt) cc_final: 0.7891 (mm) REVERT: J 122 TRP cc_start: 0.7031 (t-100) cc_final: 0.6100 (t-100) REVERT: J 317 TYR cc_start: 0.4650 (m-10) cc_final: 0.4171 (m-10) REVERT: M 122 TRP cc_start: 0.6587 (t-100) cc_final: 0.5760 (t-100) REVERT: M 301 LEU cc_start: 0.8905 (mm) cc_final: 0.8691 (mm) REVERT: M 317 TYR cc_start: 0.4311 (m-10) cc_final: 0.3810 (m-10) REVERT: N 64 PHE cc_start: 0.5666 (t80) cc_final: 0.5372 (t80) REVERT: N 122 TRP cc_start: 0.6603 (t-100) cc_final: 0.5817 (t-100) outliers start: 8 outliers final: 1 residues processed: 412 average time/residue: 0.2302 time to fit residues: 150.9930 Evaluate side-chains 257 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 254 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 351 optimal weight: 40.0000 chunk 26 optimal weight: 0.7980 chunk 286 optimal weight: 8.9990 chunk 373 optimal weight: 10.0000 chunk 424 optimal weight: 20.0000 chunk 58 optimal weight: 0.9980 chunk 122 optimal weight: 0.3980 chunk 98 optimal weight: 1.9990 chunk 218 optimal weight: 20.0000 chunk 109 optimal weight: 20.0000 chunk 227 optimal weight: 30.0000 overall best weight: 2.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 6 GLN P 6 GLN Q 160 GLN ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 HIS J 19 GLN M 19 GLN N 19 GLN N 65 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.115460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.088757 restraints weight = 156267.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.087081 restraints weight = 75339.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.087827 restraints weight = 49053.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.088080 restraints weight = 38539.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.088369 restraints weight = 33795.329| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 35298 Z= 0.192 Angle : 0.737 12.572 47988 Z= 0.380 Chirality : 0.047 0.183 5454 Planarity : 0.007 0.102 6144 Dihedral : 7.067 36.787 4878 Min Nonbonded Distance : 1.344 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.92 % Favored : 88.95 % Rotamer: Outliers : 0.10 % Allowed : 2.77 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.57 % Twisted Proline : 2.54 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.12), residues: 4488 helix: -0.05 (0.17), residues: 786 sheet: -2.77 (0.13), residues: 1236 loop : -2.08 (0.13), residues: 2466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.001 ARG L 61 TYR 0.033 0.002 TYR P 102 PHE 0.027 0.002 PHE B 64 TRP 0.029 0.002 TRP O 47 HIS 0.009 0.001 HIS R 91 Details of bonding type rmsd covalent geometry : bond 0.00429 (35274) covalent geometry : angle 0.73648 (47940) SS BOND : bond 0.00390 ( 24) SS BOND : angle 0.90845 ( 48) hydrogen bonds : bond 0.03443 ( 990) hydrogen bonds : angle 6.42228 ( 2718) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 367 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.8171 (mpp) cc_final: 0.7755 (mpp) REVERT: A 237 ASP cc_start: 0.8722 (t0) cc_final: 0.8396 (t0) REVERT: A 276 MET cc_start: 0.8177 (mpp) cc_final: 0.7962 (mpp) REVERT: A 277 GLU cc_start: 0.8678 (mm-30) cc_final: 0.7686 (mt-10) REVERT: A 279 ASN cc_start: 0.9076 (t0) cc_final: 0.8426 (t0) REVERT: D 89 ASP cc_start: 0.9065 (p0) cc_final: 0.8853 (p0) REVERT: F 206 TYR cc_start: 0.6999 (m-80) cc_final: 0.6765 (m-80) REVERT: G 145 GLU cc_start: 0.6719 (mt-10) cc_final: 0.6184 (tm-30) REVERT: K 45 LEU cc_start: 0.8346 (mp) cc_final: 0.8112 (mp) REVERT: K 98 ARG cc_start: 0.6724 (tmm160) cc_final: 0.6484 (tmm160) REVERT: K 109 GLN cc_start: 0.8236 (mt0) cc_final: 0.6757 (pm20) REVERT: K 211 ASP cc_start: 0.8084 (m-30) cc_final: 0.7272 (t0) REVERT: L 35 TRP cc_start: 0.6674 (m100) cc_final: 0.5974 (m100) REVERT: L 72 THR cc_start: 0.8095 (p) cc_final: 0.7814 (t) REVERT: L 82 ASP cc_start: 0.7903 (m-30) cc_final: 0.7630 (m-30) REVERT: O 67 ARG cc_start: 0.7406 (mtm110) cc_final: 0.6894 (mtp-110) REVERT: O 70 MET cc_start: 0.8407 (tmm) cc_final: 0.8070 (tmm) REVERT: O 81 MET cc_start: 0.8837 (ppp) cc_final: 0.8377 (tpt) REVERT: O 89 ASP cc_start: 0.8924 (p0) cc_final: 0.8451 (p0) REVERT: O 211 ASP cc_start: 0.7951 (m-30) cc_final: 0.7249 (t0) REVERT: P 113 ASP cc_start: 0.8304 (p0) cc_final: 0.7995 (p0) REVERT: P 211 ASP cc_start: 0.8270 (m-30) cc_final: 0.7857 (t0) REVERT: Q 32 TYR cc_start: 0.8336 (m-10) cc_final: 0.7905 (m-10) REVERT: Q 35 TRP cc_start: 0.6660 (m100) cc_final: 0.6129 (m100) REVERT: Q 36 TYR cc_start: 0.8541 (m-80) cc_final: 0.7819 (m-80) REVERT: Q 71 PHE cc_start: 0.8794 (m-80) cc_final: 0.8379 (m-80) REVERT: Q 82 ASP cc_start: 0.7529 (m-30) cc_final: 0.7247 (m-30) REVERT: Q 87 TYR cc_start: 0.8400 (m-80) cc_final: 0.8178 (m-80) REVERT: R 35 TRP cc_start: 0.6390 (m100) cc_final: 0.5806 (m100) REVERT: R 70 ASP cc_start: 0.8942 (t0) cc_final: 0.8718 (t0) REVERT: R 71 PHE cc_start: 0.8669 (m-10) cc_final: 0.8460 (m-10) REVERT: R 72 THR cc_start: 0.8020 (p) cc_final: 0.7807 (t) REVERT: R 82 ASP cc_start: 0.7085 (m-30) cc_final: 0.6760 (m-30) REVERT: B 15 PHE cc_start: 0.7930 (t80) cc_final: 0.7699 (t80) REVERT: B 186 GLU cc_start: 0.7962 (pt0) cc_final: 0.7751 (pt0) REVERT: B 277 GLU cc_start: 0.8685 (mm-30) cc_final: 0.7554 (mt-10) REVERT: B 279 ASN cc_start: 0.9075 (t0) cc_final: 0.8420 (t0) REVERT: C 19 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8000 (tm-30) REVERT: C 50 TYR cc_start: 0.8404 (m-80) cc_final: 0.8106 (m-10) REVERT: C 200 MET cc_start: 0.9046 (mmm) cc_final: 0.8351 (mpp) REVERT: C 274 ASP cc_start: 0.8277 (m-30) cc_final: 0.8026 (m-30) REVERT: C 279 ASN cc_start: 0.9028 (t0) cc_final: 0.8453 (t0) REVERT: J 15 PHE cc_start: 0.8821 (t80) cc_final: 0.8360 (t80) REVERT: J 43 GLN cc_start: 0.8635 (pp30) cc_final: 0.8338 (pp30) REVERT: J 95 LEU cc_start: 0.8778 (tt) cc_final: 0.7999 (mm) REVERT: J 122 TRP cc_start: 0.7248 (t-100) cc_final: 0.6143 (t-100) REVERT: J 126 HIS cc_start: 0.9002 (m90) cc_final: 0.8722 (m90) REVERT: J 218 TYR cc_start: 0.7370 (t80) cc_final: 0.7155 (t80) REVERT: J 317 TYR cc_start: 0.4861 (m-10) cc_final: 0.4335 (m-10) REVERT: M 43 GLN cc_start: 0.8537 (pp30) cc_final: 0.8186 (pp30) REVERT: M 122 TRP cc_start: 0.7302 (t-100) cc_final: 0.6139 (t-100) REVERT: M 126 HIS cc_start: 0.9047 (m90) cc_final: 0.8769 (m90) REVERT: M 218 TYR cc_start: 0.7393 (t80) cc_final: 0.7192 (t80) REVERT: N 43 GLN cc_start: 0.8813 (pp30) cc_final: 0.8474 (pp30) REVERT: N 122 TRP cc_start: 0.6812 (t-100) cc_final: 0.5871 (t-100) REVERT: N 126 HIS cc_start: 0.8769 (m90) cc_final: 0.8475 (m90) REVERT: N 218 TYR cc_start: 0.7284 (t80) cc_final: 0.7043 (t80) outliers start: 4 outliers final: 0 residues processed: 371 average time/residue: 0.2167 time to fit residues: 130.7342 Evaluate side-chains 254 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 253 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 307 optimal weight: 0.8980 chunk 154 optimal weight: 5.9990 chunk 225 optimal weight: 30.0000 chunk 57 optimal weight: 0.0070 chunk 138 optimal weight: 20.0000 chunk 194 optimal weight: 30.0000 chunk 146 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 431 optimal weight: 7.9990 chunk 298 optimal weight: 4.9990 chunk 214 optimal weight: 6.9990 overall best weight: 2.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 HIS ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 110 ASN ** Q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 HIS B 141 HIS ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 GLN ** N 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.114924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.087881 restraints weight = 154679.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.086029 restraints weight = 74761.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.086876 restraints weight = 50740.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.087108 restraints weight = 39046.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.087272 restraints weight = 34626.910| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 35298 Z= 0.198 Angle : 0.729 14.151 47988 Z= 0.373 Chirality : 0.046 0.197 5454 Planarity : 0.007 0.169 6144 Dihedral : 6.799 36.976 4878 Min Nonbonded Distance : 1.375 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.39 % Favored : 88.48 % Rotamer: Outliers : 0.03 % Allowed : 2.98 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.57 % Twisted Proline : 1.09 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.13), residues: 4488 helix: 0.36 (0.18), residues: 780 sheet: -2.60 (0.13), residues: 1236 loop : -1.99 (0.13), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 61 TYR 0.026 0.002 TYR P 102 PHE 0.028 0.002 PHE I 71 TRP 0.015 0.002 TRP F 115 HIS 0.009 0.001 HIS H 91 Details of bonding type rmsd covalent geometry : bond 0.00446 (35274) covalent geometry : angle 0.72906 (47940) SS BOND : bond 0.00419 ( 24) SS BOND : angle 0.88262 ( 48) hydrogen bonds : bond 0.03263 ( 990) hydrogen bonds : angle 6.10752 ( 2718) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 350 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ASP cc_start: 0.8727 (t0) cc_final: 0.8379 (t0) REVERT: A 277 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8342 (mm-30) REVERT: A 279 ASN cc_start: 0.9090 (t0) cc_final: 0.8453 (t0) REVERT: D 206 TYR cc_start: 0.7417 (m-80) cc_final: 0.6993 (m-80) REVERT: G 145 GLU cc_start: 0.6698 (mt-10) cc_final: 0.6288 (tm-30) REVERT: K 109 GLN cc_start: 0.8085 (mt0) cc_final: 0.7342 (tt0) REVERT: K 113 ASP cc_start: 0.8179 (p0) cc_final: 0.7752 (p0) REVERT: K 211 ASP cc_start: 0.8177 (m-30) cc_final: 0.7329 (t0) REVERT: L 35 TRP cc_start: 0.6451 (m100) cc_final: 0.5946 (m100) REVERT: L 72 THR cc_start: 0.8105 (p) cc_final: 0.7828 (t) REVERT: O 45 LEU cc_start: 0.8695 (mp) cc_final: 0.8403 (mp) REVERT: O 67 ARG cc_start: 0.7153 (mtm110) cc_final: 0.6912 (mtp-110) REVERT: O 70 MET cc_start: 0.8507 (tmm) cc_final: 0.8188 (tmm) REVERT: O 81 MET cc_start: 0.9005 (ppp) cc_final: 0.8114 (tpt) REVERT: O 211 ASP cc_start: 0.8059 (m-30) cc_final: 0.7310 (t0) REVERT: P 113 ASP cc_start: 0.8334 (p0) cc_final: 0.7658 (p0) REVERT: P 211 ASP cc_start: 0.8362 (m-30) cc_final: 0.8050 (t0) REVERT: Q 32 TYR cc_start: 0.8336 (m-10) cc_final: 0.7868 (m-10) REVERT: Q 35 TRP cc_start: 0.7161 (m100) cc_final: 0.6418 (m100) REVERT: Q 36 TYR cc_start: 0.8739 (m-80) cc_final: 0.8219 (m-80) REVERT: Q 71 PHE cc_start: 0.8724 (m-80) cc_final: 0.8195 (m-80) REVERT: R 33 LEU cc_start: 0.8385 (pp) cc_final: 0.8010 (pt) REVERT: R 35 TRP cc_start: 0.6241 (m100) cc_final: 0.5603 (m100) REVERT: R 72 THR cc_start: 0.8118 (p) cc_final: 0.7863 (t) REVERT: R 82 ASP cc_start: 0.7160 (m-30) cc_final: 0.6865 (m-30) REVERT: R 87 TYR cc_start: 0.8987 (m-10) cc_final: 0.8687 (m-80) REVERT: B 15 PHE cc_start: 0.7934 (t80) cc_final: 0.7717 (t80) REVERT: B 181 ASP cc_start: 0.7963 (t0) cc_final: 0.7751 (t0) REVERT: B 186 GLU cc_start: 0.7996 (pt0) cc_final: 0.7545 (pt0) REVERT: B 274 ASP cc_start: 0.7285 (m-30) cc_final: 0.7059 (m-30) REVERT: B 279 ASN cc_start: 0.9056 (t0) cc_final: 0.8366 (t0) REVERT: C 200 MET cc_start: 0.9059 (mmm) cc_final: 0.8793 (tpp) REVERT: C 274 ASP cc_start: 0.8299 (m-30) cc_final: 0.8037 (m-30) REVERT: C 279 ASN cc_start: 0.9060 (t0) cc_final: 0.8468 (t0) REVERT: J 15 PHE cc_start: 0.8847 (t80) cc_final: 0.8407 (t80) REVERT: J 122 TRP cc_start: 0.7214 (t-100) cc_final: 0.6181 (t-100) REVERT: J 218 TYR cc_start: 0.7459 (t80) cc_final: 0.7208 (t80) REVERT: J 317 TYR cc_start: 0.4876 (m-10) cc_final: 0.4288 (m-10) REVERT: M 43 GLN cc_start: 0.8516 (pp30) cc_final: 0.8205 (pp30) REVERT: M 122 TRP cc_start: 0.7300 (t-100) cc_final: 0.6048 (t-100) REVERT: M 126 HIS cc_start: 0.9051 (m90) cc_final: 0.8807 (m90) REVERT: M 218 TYR cc_start: 0.7537 (t80) cc_final: 0.7296 (t80) REVERT: M 317 TYR cc_start: 0.4692 (m-10) cc_final: 0.4485 (m-80) REVERT: N 43 GLN cc_start: 0.8657 (pp30) cc_final: 0.8296 (pp30) REVERT: N 122 TRP cc_start: 0.6824 (t-100) cc_final: 0.5828 (t-100) REVERT: N 218 TYR cc_start: 0.7348 (t80) cc_final: 0.7096 (t80) REVERT: N 276 MET cc_start: 0.7241 (mpp) cc_final: 0.6993 (mpp) outliers start: 1 outliers final: 0 residues processed: 351 average time/residue: 0.2128 time to fit residues: 121.1418 Evaluate side-chains 247 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 367 optimal weight: 10.0000 chunk 88 optimal weight: 50.0000 chunk 242 optimal weight: 50.0000 chunk 171 optimal weight: 5.9990 chunk 303 optimal weight: 2.9990 chunk 298 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 317 optimal weight: 0.2980 chunk 43 optimal weight: 10.0000 chunk 134 optimal weight: 20.0000 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 90 GLN ** Q 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 HIS ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 143 GLN ** M 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 143 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.115737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.086164 restraints weight = 152602.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.083938 restraints weight = 79878.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.084842 restraints weight = 55721.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.084993 restraints weight = 43677.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.085108 restraints weight = 39417.626| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 35298 Z= 0.215 Angle : 0.736 12.361 47988 Z= 0.378 Chirality : 0.047 0.198 5454 Planarity : 0.006 0.096 6144 Dihedral : 6.745 37.884 4878 Min Nonbonded Distance : 1.379 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.50 % Favored : 88.39 % Rotamer: Outliers : 0.03 % Allowed : 2.09 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.57 % Twisted Proline : 1.81 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.13), residues: 4488 helix: 0.28 (0.17), residues: 816 sheet: -2.44 (0.14), residues: 1230 loop : -2.04 (0.13), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 24 TYR 0.025 0.002 TYR K 102 PHE 0.053 0.002 PHE A 64 TRP 0.022 0.002 TRP O 47 HIS 0.010 0.002 HIS C 126 Details of bonding type rmsd covalent geometry : bond 0.00478 (35274) covalent geometry : angle 0.73589 (47940) SS BOND : bond 0.00321 ( 24) SS BOND : angle 0.61499 ( 48) hydrogen bonds : bond 0.03266 ( 990) hydrogen bonds : angle 5.93530 ( 2718) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 329 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ASP cc_start: 0.8705 (t0) cc_final: 0.8388 (t0) REVERT: A 279 ASN cc_start: 0.9130 (t0) cc_final: 0.8660 (t0) REVERT: F 48 MET cc_start: 0.8443 (mtm) cc_final: 0.7978 (mtm) REVERT: G 145 GLU cc_start: 0.6693 (mt-10) cc_final: 0.6221 (tm-30) REVERT: K 48 MET cc_start: 0.9436 (ptp) cc_final: 0.9139 (ptp) REVERT: K 109 GLN cc_start: 0.8091 (mt0) cc_final: 0.7712 (mt0) REVERT: K 113 ASP cc_start: 0.8237 (p0) cc_final: 0.7502 (p0) REVERT: K 211 ASP cc_start: 0.8032 (m-30) cc_final: 0.7164 (t0) REVERT: L 35 TRP cc_start: 0.6749 (m100) cc_final: 0.6259 (m100) REVERT: L 72 THR cc_start: 0.8038 (p) cc_final: 0.7809 (t) REVERT: O 39 GLN cc_start: 0.8731 (tp40) cc_final: 0.8055 (tp40) REVERT: O 45 LEU cc_start: 0.9026 (mp) cc_final: 0.8499 (mp) REVERT: O 67 ARG cc_start: 0.7193 (mtm110) cc_final: 0.6904 (mtp-110) REVERT: O 89 ASP cc_start: 0.8876 (p0) cc_final: 0.8329 (p0) REVERT: O 91 THR cc_start: 0.8284 (m) cc_final: 0.8046 (m) REVERT: O 109 GLN cc_start: 0.7222 (mt0) cc_final: 0.5651 (pm20) REVERT: O 211 ASP cc_start: 0.8110 (m-30) cc_final: 0.7400 (t0) REVERT: P 113 ASP cc_start: 0.8465 (p0) cc_final: 0.8167 (p0) REVERT: P 211 ASP cc_start: 0.8180 (m-30) cc_final: 0.7807 (t0) REVERT: Q 35 TRP cc_start: 0.7134 (m100) cc_final: 0.6177 (m100) REVERT: Q 36 TYR cc_start: 0.8640 (m-80) cc_final: 0.8108 (m-80) REVERT: Q 71 PHE cc_start: 0.8623 (m-80) cc_final: 0.8034 (m-80) REVERT: Q 82 ASP cc_start: 0.7677 (m-30) cc_final: 0.7331 (m-30) REVERT: R 35 TRP cc_start: 0.6229 (m100) cc_final: 0.5835 (m100) REVERT: R 36 TYR cc_start: 0.8631 (m-80) cc_final: 0.8416 (m-80) REVERT: R 72 THR cc_start: 0.8073 (p) cc_final: 0.7862 (t) REVERT: R 82 ASP cc_start: 0.7270 (m-30) cc_final: 0.6780 (m-30) REVERT: R 87 TYR cc_start: 0.8956 (m-10) cc_final: 0.8749 (m-80) REVERT: B 200 MET cc_start: 0.8050 (mpp) cc_final: 0.7810 (mpp) REVERT: B 279 ASN cc_start: 0.9049 (t0) cc_final: 0.8541 (t0) REVERT: C 176 TYR cc_start: 0.8635 (m-80) cc_final: 0.8316 (m-80) REVERT: C 200 MET cc_start: 0.9101 (mmm) cc_final: 0.8366 (mpp) REVERT: C 274 ASP cc_start: 0.8365 (m-30) cc_final: 0.8092 (m-30) REVERT: C 279 ASN cc_start: 0.9052 (t0) cc_final: 0.8602 (t0) REVERT: J 15 PHE cc_start: 0.8767 (t80) cc_final: 0.8386 (t80) REVERT: J 95 LEU cc_start: 0.8690 (tt) cc_final: 0.8035 (mm) REVERT: J 122 TRP cc_start: 0.7113 (t-100) cc_final: 0.6162 (t-100) REVERT: J 188 TYR cc_start: 0.7849 (t80) cc_final: 0.7335 (t80) REVERT: J 218 TYR cc_start: 0.7409 (t80) cc_final: 0.7154 (t80) REVERT: J 317 TYR cc_start: 0.4767 (m-10) cc_final: 0.4180 (m-10) REVERT: M 122 TRP cc_start: 0.7270 (t-100) cc_final: 0.6100 (t-100) REVERT: M 126 HIS cc_start: 0.8993 (m90) cc_final: 0.8783 (m90) REVERT: M 218 TYR cc_start: 0.7532 (t80) cc_final: 0.7277 (t80) REVERT: M 317 TYR cc_start: 0.4944 (m-10) cc_final: 0.4481 (m-80) REVERT: N 43 GLN cc_start: 0.8678 (pp30) cc_final: 0.8388 (pp30) REVERT: N 122 TRP cc_start: 0.6792 (t-100) cc_final: 0.5793 (t-100) REVERT: N 126 HIS cc_start: 0.8755 (m90) cc_final: 0.8525 (m90) REVERT: N 218 TYR cc_start: 0.7498 (t80) cc_final: 0.7217 (t80) REVERT: N 276 MET cc_start: 0.7118 (mpp) cc_final: 0.6878 (mpp) outliers start: 1 outliers final: 1 residues processed: 330 average time/residue: 0.2046 time to fit residues: 111.4542 Evaluate side-chains 241 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 240 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 250 optimal weight: 20.0000 chunk 115 optimal weight: 6.9990 chunk 285 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 167 optimal weight: 30.0000 chunk 351 optimal weight: 40.0000 chunk 21 optimal weight: 4.9990 chunk 72 optimal weight: 20.0000 chunk 403 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 HIS ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** M 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.115183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.085885 restraints weight = 154132.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.083726 restraints weight = 83502.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.083911 restraints weight = 64575.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.084434 restraints weight = 49611.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.084472 restraints weight = 41687.706| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 35298 Z= 0.245 Angle : 0.758 12.408 47988 Z= 0.388 Chirality : 0.048 0.193 5454 Planarity : 0.006 0.082 6144 Dihedral : 6.713 36.531 4878 Min Nonbonded Distance : 1.271 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.81 % Favored : 88.08 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.57 % Twisted Proline : 0.72 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.12), residues: 4488 helix: 0.26 (0.17), residues: 822 sheet: -2.29 (0.13), residues: 1296 loop : -2.21 (0.13), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG R 61 TYR 0.026 0.002 TYR H 49 PHE 0.046 0.003 PHE B 64 TRP 0.021 0.002 TRP D 115 HIS 0.009 0.002 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00541 (35274) covalent geometry : angle 0.75817 (47940) SS BOND : bond 0.00357 ( 24) SS BOND : angle 0.67774 ( 48) hydrogen bonds : bond 0.03376 ( 990) hydrogen bonds : angle 5.84698 ( 2718) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.8309 (mpp) cc_final: 0.7975 (mpp) REVERT: A 279 ASN cc_start: 0.9050 (t0) cc_final: 0.8403 (t0) REVERT: K 47 TRP cc_start: 0.7829 (t60) cc_final: 0.7607 (t60) REVERT: K 109 GLN cc_start: 0.8068 (mt0) cc_final: 0.7622 (mt0) REVERT: K 113 ASP cc_start: 0.8298 (p0) cc_final: 0.7573 (p0) REVERT: K 211 ASP cc_start: 0.7991 (m-30) cc_final: 0.7096 (t0) REVERT: L 35 TRP cc_start: 0.6840 (m100) cc_final: 0.6290 (m100) REVERT: L 71 PHE cc_start: 0.8761 (m-10) cc_final: 0.8236 (m-10) REVERT: L 72 THR cc_start: 0.7826 (p) cc_final: 0.7437 (p) REVERT: O 67 ARG cc_start: 0.7253 (mtm110) cc_final: 0.6920 (mtp-110) REVERT: O 109 GLN cc_start: 0.7358 (mt0) cc_final: 0.5885 (pm20) REVERT: O 211 ASP cc_start: 0.8131 (m-30) cc_final: 0.7424 (t0) REVERT: P 113 ASP cc_start: 0.8426 (p0) cc_final: 0.8158 (p0) REVERT: P 211 ASP cc_start: 0.8172 (m-30) cc_final: 0.7798 (t0) REVERT: Q 35 TRP cc_start: 0.7127 (m100) cc_final: 0.6242 (m100) REVERT: Q 71 PHE cc_start: 0.8351 (m-80) cc_final: 0.7760 (m-80) REVERT: Q 82 ASP cc_start: 0.7714 (m-30) cc_final: 0.7460 (m-30) REVERT: Q 210 ASN cc_start: 0.8136 (t0) cc_final: 0.7846 (t0) REVERT: R 35 TRP cc_start: 0.6341 (m100) cc_final: 0.5880 (m100) REVERT: R 72 THR cc_start: 0.7876 (p) cc_final: 0.7664 (t) REVERT: B 176 TYR cc_start: 0.8626 (m-80) cc_final: 0.8009 (m-80) REVERT: B 279 ASN cc_start: 0.9037 (t0) cc_final: 0.8455 (t0) REVERT: C 176 TYR cc_start: 0.8621 (m-80) cc_final: 0.8365 (m-80) REVERT: C 200 MET cc_start: 0.9157 (mmm) cc_final: 0.8885 (tpp) REVERT: C 237 ASP cc_start: 0.8965 (t0) cc_final: 0.8762 (t0) REVERT: C 274 ASP cc_start: 0.8417 (m-30) cc_final: 0.8096 (m-30) REVERT: C 279 ASN cc_start: 0.9114 (t0) cc_final: 0.8634 (t0) REVERT: J 15 PHE cc_start: 0.8682 (t80) cc_final: 0.8154 (t80) REVERT: J 95 LEU cc_start: 0.8724 (tt) cc_final: 0.8180 (mm) REVERT: J 122 TRP cc_start: 0.7192 (t-100) cc_final: 0.6302 (t-100) REVERT: J 188 TYR cc_start: 0.7776 (t80) cc_final: 0.7083 (t80) REVERT: J 218 TYR cc_start: 0.7451 (t80) cc_final: 0.7181 (t80) REVERT: J 317 TYR cc_start: 0.4828 (m-10) cc_final: 0.4274 (m-10) REVERT: M 122 TRP cc_start: 0.7160 (t-100) cc_final: 0.6032 (t-100) REVERT: M 218 TYR cc_start: 0.7629 (t80) cc_final: 0.7348 (t80) REVERT: N 15 PHE cc_start: 0.8852 (t80) cc_final: 0.8543 (t80) REVERT: N 43 GLN cc_start: 0.8778 (pp30) cc_final: 0.8425 (pp30) REVERT: N 122 TRP cc_start: 0.6864 (t-100) cc_final: 0.5835 (t-100) REVERT: N 218 TYR cc_start: 0.7504 (t80) cc_final: 0.7216 (t80) outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.2100 time to fit residues: 109.8852 Evaluate side-chains 220 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 442 optimal weight: 5.9990 chunk 251 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 400 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 426 optimal weight: 2.9990 chunk 415 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 375 optimal weight: 8.9990 chunk 263 optimal weight: 8.9990 chunk 417 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN ** I 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN O 6 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** M 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 111 HIS N 143 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.113655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.086324 restraints weight = 154671.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.084617 restraints weight = 77338.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.084866 restraints weight = 57956.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.085068 restraints weight = 43695.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.085281 restraints weight = 38058.868| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 35298 Z= 0.204 Angle : 0.726 13.367 47988 Z= 0.370 Chirality : 0.047 0.239 5454 Planarity : 0.006 0.096 6144 Dihedral : 6.617 37.238 4878 Min Nonbonded Distance : 1.326 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.43 % Favored : 88.46 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.57 % Twisted Proline : 1.45 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.13), residues: 4488 helix: 0.34 (0.18), residues: 822 sheet: -2.34 (0.14), residues: 1266 loop : -1.88 (0.13), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG R 61 TYR 0.044 0.002 TYR R 36 PHE 0.055 0.002 PHE B 64 TRP 0.018 0.002 TRP D 115 HIS 0.011 0.001 HIS M 312 Details of bonding type rmsd covalent geometry : bond 0.00454 (35274) covalent geometry : angle 0.72584 (47940) SS BOND : bond 0.00333 ( 24) SS BOND : angle 0.61821 ( 48) hydrogen bonds : bond 0.03160 ( 990) hydrogen bonds : angle 5.69186 ( 2718) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.8262 (mpp) cc_final: 0.7961 (mpp) REVERT: A 279 ASN cc_start: 0.9032 (t0) cc_final: 0.8443 (t0) REVERT: G 48 MET cc_start: 0.8566 (mtm) cc_final: 0.8194 (mtm) REVERT: K 48 MET cc_start: 0.9469 (ptp) cc_final: 0.9242 (ptp) REVERT: K 109 GLN cc_start: 0.8071 (mt0) cc_final: 0.6410 (pm20) REVERT: K 211 ASP cc_start: 0.8025 (m-30) cc_final: 0.7136 (t0) REVERT: L 35 TRP cc_start: 0.7059 (m100) cc_final: 0.6414 (m100) REVERT: L 71 PHE cc_start: 0.8814 (m-10) cc_final: 0.8259 (m-10) REVERT: L 72 THR cc_start: 0.7823 (p) cc_final: 0.7446 (t) REVERT: O 67 ARG cc_start: 0.7249 (mtm110) cc_final: 0.6841 (mtp-110) REVERT: O 89 ASP cc_start: 0.8651 (p0) cc_final: 0.8142 (p0) REVERT: O 109 GLN cc_start: 0.7375 (mt0) cc_final: 0.5892 (pm20) REVERT: O 211 ASP cc_start: 0.8189 (m-30) cc_final: 0.7492 (t0) REVERT: P 45 LEU cc_start: 0.8627 (mp) cc_final: 0.8161 (mp) REVERT: P 109 GLN cc_start: 0.7923 (mt0) cc_final: 0.7601 (mt0) REVERT: P 113 ASP cc_start: 0.8429 (p0) cc_final: 0.7620 (p0) REVERT: P 211 ASP cc_start: 0.8241 (m-30) cc_final: 0.7859 (t0) REVERT: Q 35 TRP cc_start: 0.7166 (m100) cc_final: 0.6201 (m100) REVERT: Q 36 TYR cc_start: 0.8621 (m-80) cc_final: 0.8304 (m-80) REVERT: Q 71 PHE cc_start: 0.8469 (m-80) cc_final: 0.7835 (m-80) REVERT: Q 82 ASP cc_start: 0.7695 (m-30) cc_final: 0.7439 (m-30) REVERT: Q 210 ASN cc_start: 0.8190 (t0) cc_final: 0.7900 (t0) REVERT: R 35 TRP cc_start: 0.6526 (m100) cc_final: 0.6102 (m100) REVERT: R 72 THR cc_start: 0.7942 (p) cc_final: 0.7676 (t) REVERT: R 82 ASP cc_start: 0.7690 (m-30) cc_final: 0.7445 (m-30) REVERT: B 176 TYR cc_start: 0.8550 (m-80) cc_final: 0.7971 (m-80) REVERT: B 279 ASN cc_start: 0.9001 (t0) cc_final: 0.8468 (t0) REVERT: C 176 TYR cc_start: 0.8550 (m-80) cc_final: 0.8292 (m-80) REVERT: C 200 MET cc_start: 0.9123 (mmm) cc_final: 0.8836 (tpp) REVERT: C 237 ASP cc_start: 0.8973 (t0) cc_final: 0.8768 (t0) REVERT: C 274 ASP cc_start: 0.8461 (m-30) cc_final: 0.8155 (m-30) REVERT: C 279 ASN cc_start: 0.9072 (t0) cc_final: 0.8602 (t0) REVERT: J 15 PHE cc_start: 0.8770 (t80) cc_final: 0.8214 (t80) REVERT: J 95 LEU cc_start: 0.8760 (tt) cc_final: 0.7962 (mm) REVERT: J 105 ILE cc_start: 0.8874 (mp) cc_final: 0.8490 (pt) REVERT: J 122 TRP cc_start: 0.7244 (t-100) cc_final: 0.6222 (t-100) REVERT: J 218 TYR cc_start: 0.7567 (t80) cc_final: 0.7261 (t80) REVERT: J 304 PHE cc_start: 0.8184 (m-80) cc_final: 0.7181 (m-80) REVERT: M 122 TRP cc_start: 0.7161 (t-100) cc_final: 0.6046 (t-100) REVERT: M 218 TYR cc_start: 0.7774 (t80) cc_final: 0.7459 (t80) REVERT: M 317 TYR cc_start: 0.4639 (m-10) cc_final: 0.4439 (m-80) REVERT: N 15 PHE cc_start: 0.8869 (t80) cc_final: 0.8511 (t80) REVERT: N 122 TRP cc_start: 0.6949 (t-100) cc_final: 0.5858 (t-100) REVERT: N 218 TYR cc_start: 0.7644 (t80) cc_final: 0.7329 (t80) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.2037 time to fit residues: 108.1166 Evaluate side-chains 229 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 180 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 23 optimal weight: 0.0980 chunk 92 optimal weight: 2.9990 chunk 277 optimal weight: 7.9990 chunk 161 optimal weight: 0.7980 chunk 138 optimal weight: 7.9990 chunk 221 optimal weight: 20.0000 chunk 144 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 307 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN L 138 ASN P 6 GLN P 110 ASN ** Q 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** M 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.114386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.087223 restraints weight = 154940.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.085270 restraints weight = 75325.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.086176 restraints weight = 49150.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.086262 restraints weight = 39139.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.086418 restraints weight = 35061.591| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 35298 Z= 0.159 Angle : 0.704 13.510 47988 Z= 0.358 Chirality : 0.047 0.260 5454 Planarity : 0.006 0.117 6144 Dihedral : 6.498 38.280 4878 Min Nonbonded Distance : 1.367 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.19 % Favored : 88.73 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.57 % Twisted Proline : 1.45 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.13), residues: 4488 helix: 0.45 (0.18), residues: 822 sheet: -2.21 (0.14), residues: 1254 loop : -1.79 (0.14), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 61 TYR 0.033 0.002 TYR R 36 PHE 0.044 0.002 PHE B 64 TRP 0.020 0.002 TRP F 111 HIS 0.009 0.001 HIS H 91 Details of bonding type rmsd covalent geometry : bond 0.00362 (35274) covalent geometry : angle 0.70447 (47940) SS BOND : bond 0.00306 ( 24) SS BOND : angle 0.62868 ( 48) hydrogen bonds : bond 0.03008 ( 990) hydrogen bonds : angle 5.54842 ( 2718) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.8196 (mpp) cc_final: 0.7897 (mpp) REVERT: A 279 ASN cc_start: 0.9003 (t0) cc_final: 0.8462 (t0) REVERT: K 62 GLN cc_start: 0.9040 (tp40) cc_final: 0.8658 (tm-30) REVERT: K 109 GLN cc_start: 0.7830 (mt0) cc_final: 0.6268 (pm20) REVERT: K 211 ASP cc_start: 0.7996 (m-30) cc_final: 0.7120 (t0) REVERT: L 35 TRP cc_start: 0.6940 (m100) cc_final: 0.6686 (m100) REVERT: L 71 PHE cc_start: 0.8804 (m-10) cc_final: 0.8449 (m-10) REVERT: L 72 THR cc_start: 0.7679 (p) cc_final: 0.7408 (t) REVERT: O 67 ARG cc_start: 0.7218 (mtm110) cc_final: 0.6689 (ptm160) REVERT: O 109 GLN cc_start: 0.7371 (mt0) cc_final: 0.5928 (pm20) REVERT: O 211 ASP cc_start: 0.8168 (m-30) cc_final: 0.7478 (t0) REVERT: P 45 LEU cc_start: 0.8685 (mp) cc_final: 0.8228 (mp) REVERT: P 109 GLN cc_start: 0.7758 (mt0) cc_final: 0.7448 (mt0) REVERT: P 113 ASP cc_start: 0.8356 (p0) cc_final: 0.7563 (p0) REVERT: P 211 ASP cc_start: 0.8103 (m-30) cc_final: 0.7708 (t0) REVERT: Q 32 TYR cc_start: 0.8246 (m-10) cc_final: 0.7741 (m-10) REVERT: Q 35 TRP cc_start: 0.7100 (m100) cc_final: 0.6134 (m100) REVERT: Q 70 ASP cc_start: 0.8838 (t70) cc_final: 0.8567 (t0) REVERT: Q 71 PHE cc_start: 0.8729 (m-10) cc_final: 0.7942 (m-10) REVERT: Q 82 ASP cc_start: 0.7680 (m-30) cc_final: 0.7446 (m-30) REVERT: Q 210 ASN cc_start: 0.8134 (t0) cc_final: 0.7872 (t0) REVERT: R 35 TRP cc_start: 0.6610 (m100) cc_final: 0.6122 (m100) REVERT: B 200 MET cc_start: 0.8620 (mmm) cc_final: 0.7657 (mpp) REVERT: B 279 ASN cc_start: 0.8984 (t0) cc_final: 0.8478 (t0) REVERT: C 176 TYR cc_start: 0.8545 (m-80) cc_final: 0.8315 (m-80) REVERT: C 200 MET cc_start: 0.9098 (mmm) cc_final: 0.8795 (tpp) REVERT: C 274 ASP cc_start: 0.8417 (m-30) cc_final: 0.8161 (m-30) REVERT: C 279 ASN cc_start: 0.9087 (t0) cc_final: 0.8639 (t0) REVERT: J 15 PHE cc_start: 0.8717 (t80) cc_final: 0.8392 (t80) REVERT: J 95 LEU cc_start: 0.8685 (tt) cc_final: 0.7855 (mm) REVERT: J 105 ILE cc_start: 0.8838 (mp) cc_final: 0.8451 (pt) REVERT: J 122 TRP cc_start: 0.7099 (t-100) cc_final: 0.6109 (t-100) REVERT: J 218 TYR cc_start: 0.7623 (t80) cc_final: 0.7301 (t80) REVERT: J 304 PHE cc_start: 0.8233 (m-80) cc_final: 0.7105 (m-80) REVERT: M 15 PHE cc_start: 0.8718 (t80) cc_final: 0.8238 (t80) REVERT: M 122 TRP cc_start: 0.7093 (t-100) cc_final: 0.5977 (t-100) REVERT: M 147 PHE cc_start: 0.8843 (m-80) cc_final: 0.8583 (m-10) REVERT: M 218 TYR cc_start: 0.7716 (t80) cc_final: 0.7409 (t80) REVERT: M 317 TYR cc_start: 0.4902 (m-10) cc_final: 0.4416 (m-80) REVERT: N 15 PHE cc_start: 0.8854 (t80) cc_final: 0.8495 (t80) REVERT: N 122 TRP cc_start: 0.6944 (t-100) cc_final: 0.5863 (t-100) REVERT: N 218 TYR cc_start: 0.7675 (t80) cc_final: 0.7335 (t80) REVERT: N 229 LEU cc_start: 0.9630 (tt) cc_final: 0.9291 (mm) REVERT: N 276 MET cc_start: 0.7159 (mpp) cc_final: 0.6873 (mpp) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.1994 time to fit residues: 107.0049 Evaluate side-chains 232 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 337 optimal weight: 3.9990 chunk 326 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 194 optimal weight: 0.7980 chunk 296 optimal weight: 3.9990 chunk 233 optimal weight: 30.0000 chunk 195 optimal weight: 7.9990 chunk 336 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 208 optimal weight: 0.0370 overall best weight: 1.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 138 ASN ** M 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.114412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.087311 restraints weight = 153404.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.085442 restraints weight = 74893.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.086465 restraints weight = 50054.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.086621 restraints weight = 38036.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.086785 restraints weight = 33688.175| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35298 Z= 0.151 Angle : 0.691 12.536 47988 Z= 0.350 Chirality : 0.047 0.304 5454 Planarity : 0.006 0.084 6144 Dihedral : 6.316 38.099 4878 Min Nonbonded Distance : 1.349 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.85 % Favored : 89.08 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.57 % Twisted Proline : 1.09 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.13), residues: 4488 helix: 0.57 (0.18), residues: 822 sheet: -2.17 (0.14), residues: 1314 loop : -1.87 (0.14), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 61 TYR 0.024 0.002 TYR R 36 PHE 0.040 0.002 PHE B 64 TRP 0.017 0.002 TRP G 111 HIS 0.010 0.001 HIS H 91 Details of bonding type rmsd covalent geometry : bond 0.00345 (35274) covalent geometry : angle 0.69124 (47940) SS BOND : bond 0.00319 ( 24) SS BOND : angle 0.59488 ( 48) hydrogen bonds : bond 0.02929 ( 990) hydrogen bonds : angle 5.37452 ( 2718) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ASN cc_start: 0.8995 (t0) cc_final: 0.8520 (t0) REVERT: D 48 MET cc_start: 0.8424 (mtm) cc_final: 0.8061 (mtm) REVERT: K 47 TRP cc_start: 0.7774 (t60) cc_final: 0.7359 (t60) REVERT: K 89 ASP cc_start: 0.8965 (p0) cc_final: 0.8718 (p0) REVERT: K 90 ASP cc_start: 0.8225 (m-30) cc_final: 0.7843 (m-30) REVERT: K 109 GLN cc_start: 0.7901 (mt0) cc_final: 0.6652 (pm20) REVERT: K 211 ASP cc_start: 0.7975 (m-30) cc_final: 0.7148 (t0) REVERT: L 35 TRP cc_start: 0.7036 (m100) cc_final: 0.6281 (m100) REVERT: L 71 PHE cc_start: 0.8804 (m-10) cc_final: 0.8412 (m-10) REVERT: L 72 THR cc_start: 0.7573 (p) cc_final: 0.7197 (t) REVERT: O 109 GLN cc_start: 0.7423 (mt0) cc_final: 0.5956 (pm20) REVERT: O 211 ASP cc_start: 0.8183 (m-30) cc_final: 0.7493 (t0) REVERT: P 5 VAL cc_start: 0.8766 (t) cc_final: 0.8550 (t) REVERT: P 45 LEU cc_start: 0.8664 (mp) cc_final: 0.8080 (mp) REVERT: P 113 ASP cc_start: 0.8410 (p0) cc_final: 0.8185 (p0) REVERT: P 211 ASP cc_start: 0.8087 (m-30) cc_final: 0.7667 (t0) REVERT: Q 35 TRP cc_start: 0.7278 (m100) cc_final: 0.6650 (m100) REVERT: Q 70 ASP cc_start: 0.8889 (t70) cc_final: 0.8606 (t0) REVERT: Q 71 PHE cc_start: 0.8735 (m-10) cc_final: 0.7907 (m-10) REVERT: Q 210 ASN cc_start: 0.8115 (t0) cc_final: 0.7855 (t0) REVERT: R 35 TRP cc_start: 0.6753 (m100) cc_final: 0.6240 (m100) REVERT: R 87 TYR cc_start: 0.8733 (m-80) cc_final: 0.8431 (m-80) REVERT: B 279 ASN cc_start: 0.9011 (t0) cc_final: 0.8499 (t0) REVERT: C 103 LEU cc_start: 0.8943 (mp) cc_final: 0.8655 (mt) REVERT: C 200 MET cc_start: 0.9097 (mmm) cc_final: 0.8827 (tpp) REVERT: C 274 ASP cc_start: 0.8376 (m-30) cc_final: 0.8112 (m-30) REVERT: C 279 ASN cc_start: 0.9066 (t0) cc_final: 0.8649 (t0) REVERT: J 15 PHE cc_start: 0.8687 (t80) cc_final: 0.8304 (t80) REVERT: J 95 LEU cc_start: 0.8692 (tt) cc_final: 0.7837 (mm) REVERT: J 105 ILE cc_start: 0.8870 (mp) cc_final: 0.8489 (pt) REVERT: J 122 TRP cc_start: 0.6940 (t-100) cc_final: 0.6050 (t-100) REVERT: J 218 TYR cc_start: 0.7696 (t80) cc_final: 0.7374 (t80) REVERT: J 304 PHE cc_start: 0.8245 (m-80) cc_final: 0.7029 (m-80) REVERT: M 15 PHE cc_start: 0.8721 (t80) cc_final: 0.8275 (t80) REVERT: M 105 ILE cc_start: 0.8899 (mp) cc_final: 0.8506 (pt) REVERT: M 122 TRP cc_start: 0.6973 (t-100) cc_final: 0.5964 (t-100) REVERT: M 126 HIS cc_start: 0.8984 (m90) cc_final: 0.8671 (m170) REVERT: M 218 TYR cc_start: 0.7797 (t80) cc_final: 0.7496 (t80) REVERT: M 317 TYR cc_start: 0.5018 (m-10) cc_final: 0.4689 (m-10) REVERT: N 15 PHE cc_start: 0.8841 (t80) cc_final: 0.8495 (t80) REVERT: N 122 TRP cc_start: 0.6950 (t-100) cc_final: 0.5948 (t-100) REVERT: N 218 TYR cc_start: 0.7719 (t80) cc_final: 0.7362 (t80) REVERT: N 276 MET cc_start: 0.6740 (mpp) cc_final: 0.6497 (mpp) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.1991 time to fit residues: 107.0838 Evaluate side-chains 232 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 430 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 112 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 202 optimal weight: 20.0000 chunk 191 optimal weight: 10.0000 chunk 322 optimal weight: 1.9990 chunk 260 optimal weight: 20.0000 chunk 80 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 437 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 HIS ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN O 39 GLN P 39 GLN ** Q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** M 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 294 ASN N 294 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.113514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.086265 restraints weight = 155046.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.084412 restraints weight = 75636.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.085204 restraints weight = 50800.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.085405 restraints weight = 40352.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.085465 restraints weight = 36391.757| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 35298 Z= 0.205 Angle : 0.727 12.486 47988 Z= 0.370 Chirality : 0.047 0.238 5454 Planarity : 0.006 0.082 6144 Dihedral : 6.376 36.921 4878 Min Nonbonded Distance : 1.301 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.74 % Favored : 88.19 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.57 % Twisted Proline : 1.09 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.13), residues: 4488 helix: 0.51 (0.18), residues: 822 sheet: -2.02 (0.14), residues: 1362 loop : -1.92 (0.14), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG Q 96 TYR 0.026 0.002 TYR H 49 PHE 0.038 0.002 PHE B 64 TRP 0.047 0.002 TRP O 47 HIS 0.011 0.001 HIS H 91 Details of bonding type rmsd covalent geometry : bond 0.00460 (35274) covalent geometry : angle 0.72700 (47940) SS BOND : bond 0.00318 ( 24) SS BOND : angle 0.66827 ( 48) hydrogen bonds : bond 0.03113 ( 990) hydrogen bonds : angle 5.38795 ( 2718) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ASN cc_start: 0.9036 (t0) cc_final: 0.8529 (t0) REVERT: G 99 GLU cc_start: 0.8090 (pt0) cc_final: 0.7738 (pt0) REVERT: K 89 ASP cc_start: 0.8863 (p0) cc_final: 0.8529 (p0) REVERT: K 90 ASP cc_start: 0.8060 (m-30) cc_final: 0.7354 (m-30) REVERT: K 109 GLN cc_start: 0.7932 (mt0) cc_final: 0.7450 (mt0) REVERT: K 113 ASP cc_start: 0.7806 (p0) cc_final: 0.7105 (p0) REVERT: K 211 ASP cc_start: 0.7978 (m-30) cc_final: 0.7123 (t0) REVERT: L 35 TRP cc_start: 0.7170 (m100) cc_final: 0.6694 (m100) REVERT: L 71 PHE cc_start: 0.8847 (m-10) cc_final: 0.8423 (m-10) REVERT: L 72 THR cc_start: 0.7654 (p) cc_final: 0.7301 (t) REVERT: L 87 TYR cc_start: 0.9192 (m-10) cc_final: 0.8990 (m-80) REVERT: O 89 ASP cc_start: 0.8923 (p0) cc_final: 0.8592 (p0) REVERT: O 109 GLN cc_start: 0.7495 (mt0) cc_final: 0.6047 (pm20) REVERT: O 211 ASP cc_start: 0.8179 (m-30) cc_final: 0.7468 (t0) REVERT: P 45 LEU cc_start: 0.8677 (mp) cc_final: 0.8245 (mm) REVERT: P 109 GLN cc_start: 0.7820 (mt0) cc_final: 0.7486 (mt0) REVERT: P 113 ASP cc_start: 0.8345 (p0) cc_final: 0.7575 (p0) REVERT: P 211 ASP cc_start: 0.8092 (m-30) cc_final: 0.7652 (t0) REVERT: Q 35 TRP cc_start: 0.7516 (m100) cc_final: 0.6929 (m100) REVERT: Q 36 TYR cc_start: 0.8658 (m-80) cc_final: 0.8210 (m-80) REVERT: Q 70 ASP cc_start: 0.8884 (t70) cc_final: 0.7637 (t0) REVERT: Q 71 PHE cc_start: 0.8744 (m-10) cc_final: 0.7908 (m-10) REVERT: Q 210 ASN cc_start: 0.8187 (t0) cc_final: 0.7947 (t0) REVERT: R 35 TRP cc_start: 0.6920 (m100) cc_final: 0.6603 (m100) REVERT: R 87 TYR cc_start: 0.8786 (m-80) cc_final: 0.8479 (m-80) REVERT: B 15 PHE cc_start: 0.7913 (t80) cc_final: 0.7702 (t80) REVERT: B 276 MET cc_start: 0.8247 (mpp) cc_final: 0.7966 (mmm) REVERT: B 279 ASN cc_start: 0.8994 (t0) cc_final: 0.8482 (t0) REVERT: C 176 TYR cc_start: 0.8448 (m-80) cc_final: 0.8057 (m-80) REVERT: C 200 MET cc_start: 0.9101 (mmm) cc_final: 0.8843 (tpp) REVERT: C 274 ASP cc_start: 0.8346 (m-30) cc_final: 0.8053 (m-30) REVERT: C 279 ASN cc_start: 0.9103 (t0) cc_final: 0.8672 (t0) REVERT: J 15 PHE cc_start: 0.8661 (t80) cc_final: 0.8328 (t80) REVERT: J 95 LEU cc_start: 0.8746 (tt) cc_final: 0.7889 (mm) REVERT: J 122 TRP cc_start: 0.7060 (t-100) cc_final: 0.6066 (t-100) REVERT: J 218 TYR cc_start: 0.7736 (t80) cc_final: 0.7402 (t80) REVERT: J 304 PHE cc_start: 0.8240 (m-80) cc_final: 0.7082 (m-80) REVERT: M 15 PHE cc_start: 0.8703 (t80) cc_final: 0.8169 (t80) REVERT: M 122 TRP cc_start: 0.7090 (t-100) cc_final: 0.6156 (t-100) REVERT: M 126 HIS cc_start: 0.8927 (m90) cc_final: 0.8706 (m170) REVERT: M 218 TYR cc_start: 0.7749 (t80) cc_final: 0.7453 (t80) REVERT: M 317 TYR cc_start: 0.5107 (m-10) cc_final: 0.4779 (m-10) REVERT: N 15 PHE cc_start: 0.8830 (t80) cc_final: 0.8544 (t80) REVERT: N 122 TRP cc_start: 0.7082 (t-100) cc_final: 0.6018 (t-100) REVERT: N 212 MET cc_start: 0.9296 (mmp) cc_final: 0.9013 (ttt) REVERT: N 218 TYR cc_start: 0.7635 (t80) cc_final: 0.7291 (t80) REVERT: N 276 MET cc_start: 0.6997 (mpp) cc_final: 0.6758 (mpp) REVERT: N 294 ASN cc_start: 0.8860 (m110) cc_final: 0.8333 (t0) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.1994 time to fit residues: 102.8593 Evaluate side-chains 224 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 2 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 431 optimal weight: 6.9990 chunk 286 optimal weight: 30.0000 chunk 120 optimal weight: 6.9990 chunk 178 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 199 optimal weight: 50.0000 chunk 227 optimal weight: 20.0000 chunk 4 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN G 176 HIS ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.114223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.086492 restraints weight = 153990.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.085596 restraints weight = 101792.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.085694 restraints weight = 60536.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.086534 restraints weight = 47578.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.086552 restraints weight = 37917.338| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 35298 Z= 0.157 Angle : 0.698 15.696 47988 Z= 0.353 Chirality : 0.047 0.260 5454 Planarity : 0.006 0.080 6144 Dihedral : 6.261 38.504 4878 Min Nonbonded Distance : 1.355 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.87 % Favored : 89.06 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.57 % Twisted Proline : 0.72 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.13), residues: 4488 helix: 0.63 (0.18), residues: 822 sheet: -2.01 (0.14), residues: 1278 loop : -1.84 (0.13), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 61 TYR 0.022 0.002 TYR H 49 PHE 0.035 0.002 PHE B 64 TRP 0.017 0.002 TRP G 111 HIS 0.007 0.001 HIS C 126 Details of bonding type rmsd covalent geometry : bond 0.00356 (35274) covalent geometry : angle 0.69816 (47940) SS BOND : bond 0.00405 ( 24) SS BOND : angle 0.67711 ( 48) hydrogen bonds : bond 0.02916 ( 990) hydrogen bonds : angle 5.25549 ( 2718) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5758.05 seconds wall clock time: 101 minutes 25.55 seconds (6085.55 seconds total)