Starting phenix.real_space_refine on Sun Aug 24 01:33:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hfs_34726/08_2025/8hfs_34726.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hfs_34726/08_2025/8hfs_34726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hfs_34726/08_2025/8hfs_34726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hfs_34726/08_2025/8hfs_34726.map" model { file = "/net/cci-nas-00/data/ceres_data/8hfs_34726/08_2025/8hfs_34726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hfs_34726/08_2025/8hfs_34726.cif" } resolution = 2.98 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= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 10627 2.51 5 N 2674 2.21 5 O 2843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16216 Number of models: 1 Model: "" Number of chains: 11 Chain: "Y" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1799 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 9, 'TRANS': 239} Chain: "Z" Number of atoms: 2341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2341 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 14, 'TRANS': 288} Chain: "B" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 731 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "A" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 409 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "E" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1795 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 9, 'TRANS': 238} Chain: "F" Number of atoms: 2332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2332 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 14, 'TRANS': 287} Chain: "C" Number of atoms: 3092 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1795 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 9, 'TRANS': 238} Conformer: "B" Number of residues, atoms: 248, 1795 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 9, 'TRANS': 238} bond proxies already assigned to first conformer: 508 Chain: "D" Number of atoms: 3669 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 302, 2332 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 14, 'TRANS': 287} Conformer: "B" Number of residues, atoms: 302, 2332 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 14, 'TRANS': 287} bond proxies already assigned to first conformer: 1014 Chain: "Z" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 24 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 352 residue: pdb=" N AMET C 1 " occ=0.48 ... (14 atoms not shown) pdb=" CE BMET C 1 " occ=0.52 residue: pdb=" N AGLU C 2 " occ=0.48 ... (16 atoms not shown) pdb=" OE2BGLU C 2 " occ=0.52 residue: pdb=" N ATYR C 3 " occ=0.48 ... (22 atoms not shown) pdb=" OH BTYR C 3 " occ=0.52 residue: pdb=" N AGLY C 4 " occ=0.48 ... (6 atoms not shown) pdb=" O BGLY C 4 " occ=0.52 residue: pdb=" N AVAL C 5 " occ=0.48 ... (12 atoms not shown) pdb=" CG2BVAL C 5 " occ=0.52 residue: pdb=" N ALEU C 6 " occ=0.48 ... (14 atoms not shown) pdb=" CD2BLEU C 6 " occ=0.52 residue: pdb=" N ASER C 7 " occ=0.48 ... (10 atoms not shown) pdb=" OG BSER C 7 " occ=0.52 residue: pdb=" N AVAL C 8 " occ=0.48 ... (12 atoms not shown) pdb=" CG2BVAL C 8 " occ=0.52 residue: pdb=" N AILE C 9 " occ=0.48 ... (14 atoms not shown) pdb=" CD1BILE C 9 " occ=0.52 residue: pdb=" N ALEU C 10 " occ=0.48 ... (14 atoms not shown) pdb=" CD2BLEU C 10 " occ=0.52 residue: pdb=" N AVAL C 11 " occ=0.48 ... (12 atoms not shown) pdb=" CG2BVAL C 11 " occ=0.52 residue: pdb=" N AILE C 12 " occ=0.48 ... (14 atoms not shown) pdb=" CD1BILE C 12 " occ=0.52 ... (remaining 340 not shown) Time building chain proxies: 4.31, per 1000 atoms: 0.27 Number of scatterers: 16216 At special positions: 0 Unit cell: (131.052, 127.83, 111.717, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 2843 8.00 N 2674 7.00 C 10627 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.40 Conformation dependent library (CDL) restraints added in 739.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3854 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 4 sheets defined 75.6% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'Y' and resid 4 through 25 removed outlier: 3.511A pdb=" N VAL Y 8 " --> pdb=" O GLY Y 4 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE Y 23 " --> pdb=" O GLY Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 31 through 43 removed outlier: 4.042A pdb=" N SER Y 37 " --> pdb=" O ILE Y 33 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR Y 43 " --> pdb=" O ILE Y 39 " (cutoff:3.500A) Processing helix chain 'Y' and resid 45 through 61 removed outlier: 3.844A pdb=" N GLY Y 49 " --> pdb=" O HIS Y 45 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU Y 58 " --> pdb=" O GLY Y 54 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE Y 59 " --> pdb=" O SER Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 73 through 88 removed outlier: 3.731A pdb=" N ALA Y 77 " --> pdb=" O ASP Y 73 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER Y 82 " --> pdb=" O SER Y 78 " (cutoff:3.500A) Processing helix chain 'Y' and resid 93 through 135 removed outlier: 4.198A pdb=" N MET Y 97 " --> pdb=" O LEU Y 93 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N VAL Y 101 " --> pdb=" O MET Y 97 " (cutoff:3.500A) Proline residue: Y 102 - end of helix removed outlier: 4.046A pdb=" N VAL Y 123 " --> pdb=" O ARG Y 119 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL Y 124 " --> pdb=" O MET Y 120 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU Y 125 " --> pdb=" O LEU Y 121 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN Y 135 " --> pdb=" O ARG Y 131 " (cutoff:3.500A) Processing helix chain 'Y' and resid 137 through 166 removed outlier: 3.618A pdb=" N VAL Y 141 " --> pdb=" O SER Y 137 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE Y 156 " --> pdb=" O GLN Y 152 " (cutoff:3.500A) Proline residue: Y 159 - end of helix Processing helix chain 'Y' and resid 167 through 178 removed outlier: 4.059A pdb=" N ILE Y 171 " --> pdb=" O SER Y 167 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN Y 172 " --> pdb=" O PRO Y 168 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE Y 178 " --> pdb=" O ALA Y 174 " (cutoff:3.500A) Processing helix chain 'Y' and resid 179 through 204 removed outlier: 3.836A pdb=" N MET Y 192 " --> pdb=" O VAL Y 188 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL Y 194 " --> pdb=" O GLY Y 190 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ALA Y 195 " --> pdb=" O GLY Y 191 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL Y 196 " --> pdb=" O MET Y 192 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY Y 197 " --> pdb=" O VAL Y 193 " (cutoff:3.500A) Processing helix chain 'Y' and resid 210 through 221 Processing helix chain 'Y' and resid 227 through 249 Processing helix chain 'Z' and resid 9 through 20 Processing helix chain 'Z' and resid 21 through 23 No H-bonds generated for 'chain 'Z' and resid 21 through 23' Processing helix chain 'Z' and resid 34 through 49 Proline residue: Z 43 - end of helix Processing helix chain 'Z' and resid 52 through 63 Processing helix chain 'Z' and resid 73 through 89 removed outlier: 3.626A pdb=" N GLU Z 86 " --> pdb=" O ALA Z 82 " (cutoff:3.500A) Processing helix chain 'Z' and resid 96 through 118 removed outlier: 3.773A pdb=" N MET Z 105 " --> pdb=" O VAL Z 101 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY Z 107 " --> pdb=" O VAL Z 103 " (cutoff:3.500A) Proline residue: Z 108 - end of helix Proline residue: Z 115 - end of helix Processing helix chain 'Z' and resid 120 through 132 removed outlier: 3.698A pdb=" N ILE Z 124 " --> pdb=" O THR Z 120 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU Z 132 " --> pdb=" O ILE Z 128 " (cutoff:3.500A) Processing helix chain 'Z' and resid 138 through 167 removed outlier: 3.597A pdb=" N LEU Z 142 " --> pdb=" O ILE Z 138 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN Z 160 " --> pdb=" O LEU Z 156 " (cutoff:3.500A) Processing helix chain 'Z' and resid 170 through 175 Processing helix chain 'Z' and resid 178 through 202 removed outlier: 3.717A pdb=" N VAL Z 182 " --> pdb=" O LEU Z 178 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL Z 202 " --> pdb=" O ILE Z 198 " (cutoff:3.500A) Processing helix chain 'Z' and resid 233 through 246 removed outlier: 3.635A pdb=" N LYS Z 246 " --> pdb=" O GLN Z 242 " (cutoff:3.500A) Processing helix chain 'Z' and resid 257 through 265 Processing helix chain 'Z' and resid 267 through 283 Processing helix chain 'Z' and resid 286 through 304 removed outlier: 3.542A pdb=" N ILE Z 290 " --> pdb=" O SER Z 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 23 removed outlier: 3.962A pdb=" N GLU B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS B 22 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASP B 23 " --> pdb=" O ALA B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 41 removed outlier: 3.879A pdb=" N ASN B 30 " --> pdb=" O GLN B 26 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA B 31 " --> pdb=" O GLU B 27 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN B 41 " --> pdb=" O LYS B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 55 Processing helix chain 'B' and resid 56 through 62 Processing helix chain 'B' and resid 66 through 68 No H-bonds generated for 'chain 'B' and resid 66 through 68' Processing helix chain 'B' and resid 69 through 77 removed outlier: 3.803A pdb=" N TYR B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 93 Processing helix chain 'A' and resid 29 through 48 removed outlier: 3.643A pdb=" N GLY A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 25 removed outlier: 4.242A pdb=" N ILE E 9 " --> pdb=" O VAL E 5 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE E 23 " --> pdb=" O GLY E 19 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU E 24 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 43 removed outlier: 4.164A pdb=" N SER E 37 " --> pdb=" O ILE E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 58 removed outlier: 3.846A pdb=" N GLY E 49 " --> pdb=" O HIS E 45 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU E 58 " --> pdb=" O GLY E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 88 removed outlier: 3.741A pdb=" N ALA E 77 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 100 removed outlier: 3.766A pdb=" N ILE E 100 " --> pdb=" O ILE E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 134 removed outlier: 3.848A pdb=" N VAL E 123 " --> pdb=" O ARG E 119 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU E 125 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU E 134 " --> pdb=" O ASP E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 166 removed outlier: 4.216A pdb=" N VAL E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU E 142 " --> pdb=" O TYR E 138 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA E 148 " --> pdb=" O TRP E 144 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG E 155 " --> pdb=" O CYS E 151 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE E 156 " --> pdb=" O GLN E 152 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) Proline residue: E 159 - end of helix removed outlier: 3.554A pdb=" N LEU E 164 " --> pdb=" O ALA E 160 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL E 165 " --> pdb=" O GLY E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 178 removed outlier: 3.778A pdb=" N ILE E 171 " --> pdb=" O SER E 167 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 193 Processing helix chain 'E' and resid 193 through 205 removed outlier: 4.437A pdb=" N GLY E 197 " --> pdb=" O VAL E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 220 Processing helix chain 'E' and resid 227 through 247 Processing helix chain 'F' and resid 9 through 21 Processing helix chain 'F' and resid 34 through 49 Proline residue: F 43 - end of helix Processing helix chain 'F' and resid 52 through 62 Processing helix chain 'F' and resid 73 through 90 Processing helix chain 'F' and resid 96 through 105 removed outlier: 3.843A pdb=" N MET F 105 " --> pdb=" O VAL F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 119 Proline residue: F 115 - end of helix Processing helix chain 'F' and resid 120 through 132 removed outlier: 3.839A pdb=" N ILE F 124 " --> pdb=" O THR F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 167 removed outlier: 4.050A pdb=" N LEU F 142 " --> pdb=" O ILE F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 174 Processing helix chain 'F' and resid 177 through 201 removed outlier: 3.582A pdb=" N THR F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 246 removed outlier: 4.008A pdb=" N HIS F 237 " --> pdb=" O GLY F 233 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS F 246 " --> pdb=" O GLN F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 265 Processing helix chain 'F' and resid 267 through 283 removed outlier: 3.507A pdb=" N LEU F 271 " --> pdb=" O GLY F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 304 removed outlier: 3.501A pdb=" N ILE F 290 " --> pdb=" O SER F 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 25 removed outlier: 3.533A pdb=" N AVAL C 13 " --> pdb=" O AILE C 9 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N AILE C 23 " --> pdb=" O AGLY C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 43 removed outlier: 4.107A pdb=" N ASER C 37 " --> pdb=" O AILE C 33 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N BVAL C 42 " --> pdb=" O BLEU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 61 removed outlier: 3.734A pdb=" N AILE C 51 " --> pdb=" O ASER C 47 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALEU C 52 " --> pdb=" O AALA C 48 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N AGLY C 53 " --> pdb=" O AGLY C 49 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N BLEU C 58 " --> pdb=" O BGLY C 54 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N AILE C 59 " --> pdb=" O ASER C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 88 removed outlier: 4.443A pdb=" N AALA C 77 " --> pdb=" O AASP C 73 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N AILE C 79 " --> pdb=" O AALA C 75 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALEU C 84 " --> pdb=" O AALA C 80 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N AMET C 85 " --> pdb=" O ASER C 81 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N AVAL C 86 " --> pdb=" O ASER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'C' and resid 100 through 134 removed outlier: 3.536A pdb=" N AALA C 104 " --> pdb=" O AILE C 100 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N AILE C 105 " --> pdb=" O AVAL C 101 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALEU C 106 " --> pdb=" O APRO C 102 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N AVAL C 113 " --> pdb=" O ATHR C 109 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N BSER C 122 " --> pdb=" O BVAL C 118 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N AVAL C 123 " --> pdb=" O AARG C 119 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N AVAL C 124 " --> pdb=" O AMET C 120 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALEU C 125 " --> pdb=" O ALEU C 121 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N AGLU C 134 " --> pdb=" O AASP C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 166 removed outlier: 3.996A pdb=" N BARG C 155 " --> pdb=" O BCYS C 151 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N AILE C 156 " --> pdb=" O AGLN C 152 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N BALA C 157 " --> pdb=" O BGLY C 153 " (cutoff:3.500A) Proline residue: C 159 - end of helix Processing helix chain 'C' and resid 167 through 178 removed outlier: 3.940A pdb=" N AILE C 171 " --> pdb=" O ASER C 167 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N BILE C 178 " --> pdb=" O BALA C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 193 Processing helix chain 'C' and resid 193 through 205 removed outlier: 4.228A pdb=" N GLY C 197 " --> pdb=" O VAL C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 221 Processing helix chain 'C' and resid 227 through 247 Processing helix chain 'D' and resid 9 through 20 Processing helix chain 'D' and resid 21 through 23 No H-bonds generated for 'chain 'D' and resid 21 through 23' Processing helix chain 'D' and resid 34 through 49 removed outlier: 3.678A pdb=" N AALA D 38 " --> pdb=" O AASN D 34 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N BLEU D 41 " --> pdb=" O BTRP D 37 " (cutoff:3.500A) Proline residue: D 43 - end of helix removed outlier: 3.743A pdb=" N BLYS D 46 " --> pdb=" O BILE D 42 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N BLYS D 47 " --> pdb=" O BPRO D 43 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N BLEU D 48 " --> pdb=" O BALA D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 61 removed outlier: 4.318A pdb=" N BLYS D 56 " --> pdb=" O BGLY D 52 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N BGLU D 57 " --> pdb=" O BGLU D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 90 removed outlier: 3.736A pdb=" N AASN D 89 " --> pdb=" O AGLU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 105 removed outlier: 3.600A pdb=" N BLYS D 102 " --> pdb=" O BILE D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 118 removed outlier: 3.801A pdb=" N BASP D 114 " --> pdb=" O BALA D 110 " (cutoff:3.500A) Proline residue: D 115 - end of helix Processing helix chain 'D' and resid 121 through 132 removed outlier: 3.606A pdb=" N BSER D 131 " --> pdb=" O BALA D 127 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALEU D 132 " --> pdb=" O AILE D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 167 removed outlier: 3.714A pdb=" N BPHE D 144 " --> pdb=" O BALA D 140 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N AALA D 150 " --> pdb=" O AILE D 146 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N AILE D 151 " --> pdb=" O AVAL D 147 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N AARG D 152 " --> pdb=" O ATRP D 148 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N AILE D 153 " --> pdb=" O AASN D 149 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ATRP D 157 " --> pdb=" O AILE D 153 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ATYR D 158 " --> pdb=" O AALA D 154 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N AGLN D 160 " --> pdb=" O ALEU D 156 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N BGLU D 161 " --> pdb=" O BTRP D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 201 removed outlier: 3.533A pdb=" N THR D 181 " --> pdb=" O AGLY D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 246 removed outlier: 3.588A pdb=" N LYS D 246 " --> pdb=" O GLN D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 265 Processing helix chain 'D' and resid 267 through 283 Processing helix chain 'D' and resid 286 through 304 removed outlier: 3.578A pdb=" N ILE D 290 " --> pdb=" O SER D 286 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Z' and resid 212 through 214 Processing sheet with id=AA2, first strand: chain 'A' and resid 2 through 7 removed outlier: 5.944A pdb=" N PHE A 4 " --> pdb=" O TYR A 15 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR A 15 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 212 through 217 Processing sheet with id=AA4, first strand: chain 'D' and resid 212 through 217 removed outlier: 3.586A pdb=" N SER D 214 " --> pdb=" O THR D 255 " (cutoff:3.500A) 1040 hydrogen bonds defined for protein. 3114 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: 2.34 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5081 1.34 - 1.46: 3036 1.46 - 1.58: 8317 1.58 - 1.69: 0 1.69 - 1.81: 133 Bond restraints: 16567 Sorted by residual: bond pdb=" C THR B 57 " pdb=" N PRO B 58 " ideal model delta sigma weight residual 1.336 1.378 -0.042 1.20e-02 6.94e+03 1.25e+01 bond pdb=" CA MET C 205 " pdb=" CB MET C 205 " ideal model delta sigma weight residual 1.528 1.560 -0.032 1.51e-02 4.39e+03 4.45e+00 bond pdb=" C ILE F 42 " pdb=" N PRO F 43 " ideal model delta sigma weight residual 1.335 1.357 -0.023 1.28e-02 6.10e+03 3.16e+00 bond pdb=" C5 MAN Z 401 " pdb=" O5 MAN Z 401 " ideal model delta sigma weight residual 1.418 1.447 -0.029 2.00e-02 2.50e+03 2.18e+00 bond pdb=" C1 MAN Z 401 " pdb=" C2 MAN Z 401 " ideal model delta sigma weight residual 1.526 1.555 -0.029 2.00e-02 2.50e+03 2.13e+00 ... (remaining 16562 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 22359 2.88 - 5.75: 186 5.75 - 8.63: 16 8.63 - 11.50: 2 11.50 - 14.38: 2 Bond angle restraints: 22565 Sorted by residual: angle pdb=" C THR B 57 " pdb=" N PRO B 58 " pdb=" CA PRO B 58 " ideal model delta sigma weight residual 118.85 113.11 5.74 1.09e+00 8.42e-01 2.78e+01 angle pdb=" CG1 ILE D 204 " pdb=" CB ILE D 204 " pdb=" CG2 ILE D 204 " ideal model delta sigma weight residual 110.70 96.32 14.38 3.00e+00 1.11e-01 2.30e+01 angle pdb=" N AVAL D 116 " pdb=" CA AVAL D 116 " pdb=" C AVAL D 116 " ideal model delta sigma weight residual 113.53 109.22 4.31 9.80e-01 1.04e+00 1.94e+01 angle pdb=" N ILE Y 156 " pdb=" CA ILE Y 156 " pdb=" C ILE Y 156 " ideal model delta sigma weight residual 112.96 109.02 3.94 1.00e+00 1.00e+00 1.55e+01 angle pdb=" CA GLU F 57 " pdb=" CB GLU F 57 " pdb=" CG GLU F 57 " ideal model delta sigma weight residual 114.10 121.89 -7.79 2.00e+00 2.50e-01 1.52e+01 ... (remaining 22560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.14: 8442 18.14 - 36.28: 949 36.28 - 54.42: 253 54.42 - 72.56: 32 72.56 - 90.70: 27 Dihedral angle restraints: 9703 sinusoidal: 3658 harmonic: 6045 Sorted by residual: dihedral pdb=" CA ARG B 63 " pdb=" C ARG B 63 " pdb=" N THR B 64 " pdb=" CA THR B 64 " ideal model delta harmonic sigma weight residual -180.00 -152.55 -27.45 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA MET C 192 " pdb=" C MET C 192 " pdb=" N VAL C 193 " pdb=" CA VAL C 193 " ideal model delta harmonic sigma weight residual 180.00 -157.92 -22.08 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA MET F 32 " pdb=" C MET F 32 " pdb=" N GLN F 33 " pdb=" CA GLN F 33 " ideal model delta harmonic sigma weight residual 180.00 160.12 19.88 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 9700 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2244 0.054 - 0.107: 415 0.107 - 0.161: 47 0.161 - 0.214: 0 0.214 - 0.268: 1 Chirality restraints: 2707 Sorted by residual: chirality pdb=" CB ILE D 204 " pdb=" CA ILE D 204 " pdb=" CG1 ILE D 204 " pdb=" CG2 ILE D 204 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA LEU C 186 " pdb=" N LEU C 186 " pdb=" C LEU C 186 " pdb=" CB LEU C 186 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CA PRO Y 72 " pdb=" N PRO Y 72 " pdb=" C PRO Y 72 " pdb=" CB PRO Y 72 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 5.96e-01 ... (remaining 2704 not shown) Planarity restraints: 2790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 208 " 0.054 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO D 209 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO D 209 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 209 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR F 49 " 0.051 5.00e-02 4.00e+02 7.81e-02 9.77e+00 pdb=" N PRO F 50 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO F 50 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO F 50 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA Y 71 " 0.043 5.00e-02 4.00e+02 6.56e-02 6.89e+00 pdb=" N PRO Y 72 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO Y 72 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO Y 72 " 0.036 5.00e-02 4.00e+02 ... (remaining 2787 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 465 2.71 - 3.26: 17449 3.26 - 3.81: 27732 3.81 - 4.35: 33593 4.35 - 4.90: 56210 Nonbonded interactions: 135449 Sorted by model distance: nonbonded pdb=" O APRO D 115 " pdb=" OG1ATHR D 120 " model vdw 2.164 3.040 nonbonded pdb=" OD2 ASP F 114 " pdb=" O6 MAN F 401 " model vdw 2.173 3.040 nonbonded pdb=" OG SER B 25 " pdb=" OE1 GLU B 28 " model vdw 2.177 3.040 nonbonded pdb=" OD2 ASP Y 130 " pdb=" NH2 ARG Z 31 " model vdw 2.181 3.120 nonbonded pdb=" OG SER Y 122 " pdb=" O TRP Z 27 " model vdw 2.188 3.040 ... (remaining 135444 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and resid 180 through 248) selection = (chain 'E' and resid 180 through 248) selection = (chain 'Y' and resid 180 through 248) } ncs_group { reference = (chain 'D' and resid 178 through 307) selection = (chain 'F' and resid 178 through 307) selection = (chain 'Z' and resid 178 through 307) } 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=0.46 max=1.00 mean=0.84 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.480 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 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 : 0.003 0.042 16567 Z= 0.151 Angle : 0.648 14.381 22565 Z= 0.339 Chirality : 0.040 0.268 2707 Planarity : 0.005 0.082 2790 Dihedral : 16.845 90.700 5849 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.28 % Allowed : 24.39 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 aren not related in a simple way. whole: 0.18 (0.19), residues: 2133 helix: 0.93 (0.14), residues: 1514 sheet: -0.67 (1.17), residues: 26 loop : -1.95 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Y 131 TYR 0.022 0.001 TYR Z 49 PHE 0.009 0.001 PHE C 213 TRP 0.042 0.001 TRP F 201 HIS 0.007 0.001 HIS D 237 Details of bonding type rmsd covalent geometry : bond 0.00324 (16567) covalent geometry : angle 0.64825 (22565) hydrogen bonds : bond 0.12151 ( 1040) hydrogen bonds : angle 5.45482 ( 3114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.417 Fit side-chains REVERT: Z 230 SER cc_start: 0.7763 (t) cc_final: 0.7530 (p) REVERT: E 121 LEU cc_start: 0.8422 (tm) cc_final: 0.8177 (tt) REVERT: F 84 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7423 (mm-30) REVERT: F 86 GLU cc_start: 0.6844 (tt0) cc_final: 0.6593 (tt0) outliers start: 32 outliers final: 26 residues processed: 166 average time/residue: 0.5211 time to fit residues: 97.2796 Evaluate side-chains 158 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Y residue 45 HIS Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 165 VAL Chi-restraints excluded: chain Y residue 234 LEU Chi-restraints excluded: chain Z residue 42 ILE Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 216 ILE Chi-restraints excluded: chain Z residue 234 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 165 LYS Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 231 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 ASN C 89 ASN A ** C 135 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 HIS A ** D 67 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.164369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.137217 restraints weight = 38671.257| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.51 r_work: 0.3490 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3484 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16567 Z= 0.187 Angle : 0.657 12.760 22565 Z= 0.334 Chirality : 0.043 0.243 2707 Planarity : 0.006 0.074 2790 Dihedral : 6.335 57.384 2380 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 6.38 % Allowed : 21.88 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -0.11 (0.19), residues: 2133 helix: 0.77 (0.13), residues: 1526 sheet: -0.61 (1.38), residues: 18 loop : -2.24 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG Z 122 TYR 0.018 0.002 TYR Z 71 PHE 0.019 0.002 PHE Z 66 TRP 0.020 0.002 TRP F 201 HIS 0.006 0.001 HIS Y 145 Details of bonding type rmsd covalent geometry : bond 0.00444 (16567) covalent geometry : angle 0.65722 (22565) hydrogen bonds : bond 0.04611 ( 1040) hydrogen bonds : angle 4.63531 ( 3114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 144 time to evaluate : 0.502 Fit side-chains REVERT: Y 5 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8312 (t) REVERT: Y 106 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7635 (mm) REVERT: Z 49 TYR cc_start: 0.7101 (p90) cc_final: 0.6088 (p90) REVERT: E 120 MET cc_start: 0.5940 (OUTLIER) cc_final: 0.5418 (mtt) REVERT: E 142 GLU cc_start: 0.4790 (OUTLIER) cc_final: 0.3393 (mp0) REVERT: F 49 TYR cc_start: 0.7602 (OUTLIER) cc_final: 0.5319 (p90) REVERT: F 63 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7875 (tt) REVERT: F 84 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7540 (mm-30) outliers start: 75 outliers final: 38 residues processed: 199 average time/residue: 0.4167 time to fit residues: 95.1678 Evaluate side-chains 176 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 132 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 5 VAL Chi-restraints excluded: chain Y residue 9 ILE Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Y residue 45 HIS Chi-restraints excluded: chain Y residue 65 ASN Chi-restraints excluded: chain Y residue 106 LEU Chi-restraints excluded: chain Y residue 137 SER Chi-restraints excluded: chain Y residue 165 VAL Chi-restraints excluded: chain Y residue 204 LEU Chi-restraints excluded: chain Z residue 34 ASN Chi-restraints excluded: chain Z residue 105 MET Chi-restraints excluded: chain Z residue 106 MET Chi-restraints excluded: chain Z residue 118 TRP Chi-restraints excluded: chain Z residue 170 ILE Chi-restraints excluded: chain Z residue 216 ILE Chi-restraints excluded: chain Z residue 249 LEU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 44 TYR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain E residue 45 HIS Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 118 TRP Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 306 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 35 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 126 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 chunk 166 optimal weight: 0.0070 chunk 71 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 83 optimal weight: 0.0980 chunk 23 optimal weight: 0.8980 overall best weight: 0.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 263 GLN F 67 ASN F 205 ASN ** C 57 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 ASN B ** 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 = 0.4144 r_free = 0.4144 target = 0.169790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.140119 restraints weight = 31532.727| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.07 r_work: 0.3564 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3560 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3560 r_free = 0.3560 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3560 r_free = 0.3560 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3560 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16567 Z= 0.123 Angle : 0.581 9.994 22565 Z= 0.295 Chirality : 0.040 0.263 2707 Planarity : 0.005 0.070 2790 Dihedral : 5.370 56.258 2354 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 5.96 % Allowed : 23.55 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 aren not related in a simple way. whole: 0.20 (0.19), residues: 2133 helix: 0.99 (0.14), residues: 1541 sheet: -0.46 (1.40), residues: 18 loop : -2.23 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 61 TYR 0.008 0.001 TYR C 242 PHE 0.014 0.001 PHE E 16 TRP 0.016 0.001 TRP F 201 HIS 0.005 0.001 HIS Z 62 Details of bonding type rmsd covalent geometry : bond 0.00268 (16567) covalent geometry : angle 0.58149 (22565) hydrogen bonds : bond 0.03893 ( 1040) hydrogen bonds : angle 4.31479 ( 3114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 148 time to evaluate : 0.426 Fit side-chains REVERT: Z 49 TYR cc_start: 0.7069 (p90) cc_final: 0.6102 (p90) REVERT: Z 224 VAL cc_start: 0.9030 (t) cc_final: 0.8828 (m) REVERT: B 36 GLU cc_start: 0.7459 (tp30) cc_final: 0.7186 (mm-30) REVERT: E 120 MET cc_start: 0.5915 (OUTLIER) cc_final: 0.5333 (mtt) REVERT: E 142 GLU cc_start: 0.4491 (OUTLIER) cc_final: 0.3325 (mp0) outliers start: 63 outliers final: 26 residues processed: 193 average time/residue: 0.4503 time to fit residues: 98.6359 Evaluate side-chains 160 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Y residue 45 HIS Chi-restraints excluded: chain Z residue 42 ILE Chi-restraints excluded: chain Z residue 216 ILE Chi-restraints excluded: chain Z residue 249 LEU Chi-restraints excluded: chain Z residue 288 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 44 TYR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 45 HIS Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 214 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 121 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 123 optimal weight: 8.9990 chunk 68 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 110 optimal weight: 0.6980 chunk 81 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 263 GLN F 205 ASN F 207 ASN ** C 57 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 ASN A ** D 67 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.166272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.135911 restraints weight = 31525.976| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 1.76 r_work: 0.3544 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3420 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16567 Z= 0.157 Angle : 0.616 10.506 22565 Z= 0.312 Chirality : 0.042 0.191 2707 Planarity : 0.005 0.071 2790 Dihedral : 5.415 50.343 2353 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 7.16 % Allowed : 22.54 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 aren not related in a simple way. whole: 0.10 (0.19), residues: 2133 helix: 0.91 (0.14), residues: 1543 sheet: -0.70 (1.34), residues: 18 loop : -2.23 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 13 TYR 0.015 0.001 TYR Z 71 PHE 0.015 0.002 PHE Z 66 TRP 0.020 0.001 TRP F 201 HIS 0.006 0.001 HIS Y 145 Details of bonding type rmsd covalent geometry : bond 0.00371 (16567) covalent geometry : angle 0.61643 (22565) hydrogen bonds : bond 0.04228 ( 1040) hydrogen bonds : angle 4.35156 ( 3114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 143 time to evaluate : 0.453 Fit side-chains REVERT: Y 106 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7804 (mm) REVERT: Z 49 TYR cc_start: 0.7314 (OUTLIER) cc_final: 0.6143 (p90) REVERT: E 120 MET cc_start: 0.6021 (OUTLIER) cc_final: 0.5458 (mtt) REVERT: E 142 GLU cc_start: 0.4788 (OUTLIER) cc_final: 0.3374 (mp0) REVERT: E 205 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7346 (ptp) REVERT: F 49 TYR cc_start: 0.7871 (OUTLIER) cc_final: 0.5856 (p90) outliers start: 75 outliers final: 44 residues processed: 197 average time/residue: 0.4721 time to fit residues: 105.6373 Evaluate side-chains 182 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 132 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Y residue 45 HIS Chi-restraints excluded: chain Y residue 65 ASN Chi-restraints excluded: chain Y residue 106 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 165 VAL Chi-restraints excluded: chain Y residue 204 LEU Chi-restraints excluded: chain Y residue 234 LEU Chi-restraints excluded: chain Z residue 49 TYR Chi-restraints excluded: chain Z residue 105 MET Chi-restraints excluded: chain Z residue 118 TRP Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain Z residue 216 ILE Chi-restraints excluded: chain Z residue 249 LEU Chi-restraints excluded: chain Z residue 288 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 45 HIS Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 118 TRP Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 165 LYS Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 255 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 157 optimal weight: 0.4980 chunk 77 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 263 GLN A 25 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 ASN ** C 57 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 ASN B ** 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 = 0.4091 r_free = 0.4091 target = 0.164900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.138229 restraints weight = 29493.474| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.63 r_work: 0.3573 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16567 Z= 0.159 Angle : 0.623 10.766 22565 Z= 0.316 Chirality : 0.042 0.206 2707 Planarity : 0.005 0.072 2790 Dihedral : 5.486 52.083 2353 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 7.63 % Allowed : 23.61 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 aren not related in a simple way. whole: 0.04 (0.19), residues: 2133 helix: 0.87 (0.14), residues: 1545 sheet: -0.82 (1.30), residues: 18 loop : -2.25 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Y 131 TYR 0.015 0.001 TYR Z 71 PHE 0.013 0.002 PHE Z 66 TRP 0.021 0.001 TRP F 201 HIS 0.006 0.001 HIS Y 145 Details of bonding type rmsd covalent geometry : bond 0.00376 (16567) covalent geometry : angle 0.62324 (22565) hydrogen bonds : bond 0.04233 ( 1040) hydrogen bonds : angle 4.34715 ( 3114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 138 time to evaluate : 0.363 Fit side-chains REVERT: Z 49 TYR cc_start: 0.7153 (OUTLIER) cc_final: 0.6076 (p90) REVERT: B 43 GLU cc_start: 0.6069 (tt0) cc_final: 0.5652 (tp30) REVERT: E 120 MET cc_start: 0.6104 (OUTLIER) cc_final: 0.5530 (mtt) REVERT: E 142 GLU cc_start: 0.4807 (OUTLIER) cc_final: 0.3447 (mp0) REVERT: E 150 ILE cc_start: 0.6972 (pp) cc_final: 0.6689 (mm) REVERT: E 175 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6459 (mt) REVERT: E 205 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7239 (ptp) REVERT: F 49 TYR cc_start: 0.7865 (OUTLIER) cc_final: 0.5836 (p90) outliers start: 80 outliers final: 46 residues processed: 195 average time/residue: 0.4661 time to fit residues: 103.2539 Evaluate side-chains 186 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 134 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Y residue 45 HIS Chi-restraints excluded: chain Y residue 65 ASN Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 165 VAL Chi-restraints excluded: chain Y residue 204 LEU Chi-restraints excluded: chain Y residue 234 LEU Chi-restraints excluded: chain Z residue 34 ASN Chi-restraints excluded: chain Z residue 49 TYR Chi-restraints excluded: chain Z residue 105 MET Chi-restraints excluded: chain Z residue 118 TRP Chi-restraints excluded: chain Z residue 170 ILE Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain Z residue 216 ILE Chi-restraints excluded: chain Z residue 288 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 45 HIS Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 118 TRP Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 165 LYS Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 306 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 73 optimal weight: 0.8980 chunk 149 optimal weight: 20.0000 chunk 32 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 167 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 263 GLN F 205 ASN ** C 57 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 ASN B ** 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 = 0.4133 r_free = 0.4133 target = 0.168811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.141819 restraints weight = 34997.279| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.19 r_work: 0.3557 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16567 Z= 0.129 Angle : 0.592 10.103 22565 Z= 0.300 Chirality : 0.041 0.312 2707 Planarity : 0.005 0.071 2790 Dihedral : 5.385 54.465 2353 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 7.10 % Allowed : 24.39 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 aren not related in a simple way. whole: 0.20 (0.19), residues: 2133 helix: 0.99 (0.14), residues: 1549 sheet: -0.75 (1.32), residues: 18 loop : -2.24 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Y 131 TYR 0.009 0.001 TYR Z 71 PHE 0.010 0.001 PHE E 16 TRP 0.020 0.001 TRP F 201 HIS 0.004 0.001 HIS Z 62 Details of bonding type rmsd covalent geometry : bond 0.00291 (16567) covalent geometry : angle 0.59153 (22565) hydrogen bonds : bond 0.03881 ( 1040) hydrogen bonds : angle 4.20792 ( 3114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 147 time to evaluate : 0.430 Fit side-chains REVERT: Y 39 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8098 (mp) REVERT: Y 106 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7764 (mm) REVERT: Z 49 TYR cc_start: 0.7208 (OUTLIER) cc_final: 0.6098 (p90) REVERT: B 13 ARG cc_start: 0.7181 (mtt-85) cc_final: 0.6831 (mtt-85) REVERT: E 25 ASP cc_start: 0.7322 (t70) cc_final: 0.6866 (t0) REVERT: E 120 MET cc_start: 0.6272 (OUTLIER) cc_final: 0.5668 (mtt) REVERT: E 142 GLU cc_start: 0.4720 (OUTLIER) cc_final: 0.3392 (mp0) REVERT: E 150 ILE cc_start: 0.6967 (pp) cc_final: 0.6694 (mm) REVERT: E 175 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6495 (mt) REVERT: E 205 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7384 (ptp) REVERT: E 225 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8179 (mt-10) REVERT: F 49 TYR cc_start: 0.7926 (OUTLIER) cc_final: 0.5914 (p90) REVERT: C 225 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8200 (mt-10) outliers start: 70 outliers final: 36 residues processed: 198 average time/residue: 0.4739 time to fit residues: 106.8592 Evaluate side-chains 180 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 134 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Y residue 45 HIS Chi-restraints excluded: chain Y residue 106 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 166 ILE Chi-restraints excluded: chain Y residue 234 LEU Chi-restraints excluded: chain Z residue 34 ASN Chi-restraints excluded: chain Z residue 42 ILE Chi-restraints excluded: chain Z residue 49 TYR Chi-restraints excluded: chain Z residue 118 TRP Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain Z residue 214 SER Chi-restraints excluded: chain Z residue 216 ILE Chi-restraints excluded: chain Z residue 249 LEU Chi-restraints excluded: chain Z residue 288 ILE Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain E residue 45 HIS Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 118 TRP Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 306 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 59 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 160 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 152 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 112 optimal weight: 0.0370 chunk 167 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 128 GLN Z 263 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 ASN ** C 57 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 ASN B ** 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 = 0.4101 r_free = 0.4101 target = 0.165797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.139043 restraints weight = 30469.136| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.76 r_work: 0.3577 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3463 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16567 Z= 0.139 Angle : 0.620 12.122 22565 Z= 0.310 Chirality : 0.042 0.330 2707 Planarity : 0.005 0.071 2790 Dihedral : 5.411 55.303 2353 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 6.98 % Allowed : 24.99 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 aren not related in a simple way. whole: 0.19 (0.19), residues: 2133 helix: 1.05 (0.14), residues: 1527 sheet: -0.03 (1.53), residues: 13 loop : -2.35 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 61 TYR 0.011 0.001 TYR Z 71 PHE 0.010 0.001 PHE Z 66 TRP 0.024 0.001 TRP F 201 HIS 0.004 0.001 HIS Y 145 Details of bonding type rmsd covalent geometry : bond 0.00324 (16567) covalent geometry : angle 0.61957 (22565) hydrogen bonds : bond 0.03968 ( 1040) hydrogen bonds : angle 4.22554 ( 3114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 142 time to evaluate : 0.365 Fit side-chains REVERT: Y 39 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8123 (mp) REVERT: Y 106 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7805 (mm) REVERT: Z 49 TYR cc_start: 0.7169 (OUTLIER) cc_final: 0.6060 (p90) REVERT: B 43 GLU cc_start: 0.6631 (tp30) cc_final: 0.6391 (mm-30) REVERT: E 25 ASP cc_start: 0.6924 (t70) cc_final: 0.6684 (t70) REVERT: E 120 MET cc_start: 0.6241 (OUTLIER) cc_final: 0.5626 (mtt) REVERT: E 142 GLU cc_start: 0.4688 (OUTLIER) cc_final: 0.3411 (mp0) REVERT: E 175 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6502 (mt) REVERT: E 205 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7246 (ptp) REVERT: F 49 TYR cc_start: 0.7899 (OUTLIER) cc_final: 0.5936 (p90) REVERT: C 225 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8144 (mt-10) outliers start: 68 outliers final: 43 residues processed: 196 average time/residue: 0.4745 time to fit residues: 105.7285 Evaluate side-chains 185 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 133 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Y residue 45 HIS Chi-restraints excluded: chain Y residue 106 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 166 ILE Chi-restraints excluded: chain Y residue 181 VAL Chi-restraints excluded: chain Y residue 229 ILE Chi-restraints excluded: chain Y residue 234 LEU Chi-restraints excluded: chain Z residue 34 ASN Chi-restraints excluded: chain Z residue 42 ILE Chi-restraints excluded: chain Z residue 49 TYR Chi-restraints excluded: chain Z residue 118 TRP Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain Z residue 214 SER Chi-restraints excluded: chain Z residue 216 ILE Chi-restraints excluded: chain Z residue 288 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 45 HIS Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 118 TRP Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 165 LYS Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 306 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 65 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 79 optimal weight: 0.0770 chunk 89 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 149 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 121 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 128 GLN Z 263 GLN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 ASN ** C 57 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 ASN B ** 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 = 0.4143 r_free = 0.4143 target = 0.169837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.144203 restraints weight = 31488.546| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.68 r_work: 0.3601 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3480 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16567 Z= 0.124 Angle : 0.607 12.058 22565 Z= 0.303 Chirality : 0.041 0.337 2707 Planarity : 0.005 0.070 2790 Dihedral : 5.284 57.044 2350 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 6.50 % Allowed : 25.34 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 aren not related in a simple way. whole: 0.27 (0.19), residues: 2133 helix: 1.10 (0.14), residues: 1536 sheet: -0.01 (1.50), residues: 13 loop : -2.35 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Y 131 TYR 0.016 0.001 TYR B 44 PHE 0.022 0.001 PHE F 226 TRP 0.027 0.001 TRP F 201 HIS 0.003 0.001 HIS Z 62 Details of bonding type rmsd covalent geometry : bond 0.00281 (16567) covalent geometry : angle 0.60739 (22565) hydrogen bonds : bond 0.03766 ( 1040) hydrogen bonds : angle 4.15524 ( 3114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 139 time to evaluate : 0.553 Fit side-chains REVERT: Y 39 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.7999 (mp) REVERT: Y 147 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8138 (mt) REVERT: Z 49 TYR cc_start: 0.7155 (OUTLIER) cc_final: 0.6052 (p90) REVERT: B 43 GLU cc_start: 0.6529 (tp30) cc_final: 0.6320 (mm-30) REVERT: E 120 MET cc_start: 0.6167 (OUTLIER) cc_final: 0.5553 (mtt) REVERT: E 142 GLU cc_start: 0.4538 (OUTLIER) cc_final: 0.3361 (mp0) REVERT: E 175 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6514 (mt) REVERT: E 205 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7324 (ptp) REVERT: F 49 TYR cc_start: 0.7858 (OUTLIER) cc_final: 0.5956 (p90) outliers start: 59 outliers final: 38 residues processed: 183 average time/residue: 0.4575 time to fit residues: 94.8356 Evaluate side-chains 177 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 131 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Y residue 45 HIS Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 147 ILE Chi-restraints excluded: chain Y residue 166 ILE Chi-restraints excluded: chain Y residue 181 VAL Chi-restraints excluded: chain Y residue 229 ILE Chi-restraints excluded: chain Y residue 234 LEU Chi-restraints excluded: chain Z residue 34 ASN Chi-restraints excluded: chain Z residue 42 ILE Chi-restraints excluded: chain Z residue 49 TYR Chi-restraints excluded: chain Z residue 105 MET Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain Z residue 216 ILE Chi-restraints excluded: chain Z residue 288 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain E residue 45 HIS Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 118 TRP Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 165 LYS Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 306 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 4 optimal weight: 0.0870 chunk 38 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 128 GLN Z 263 GLN ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 ASN ** C 57 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 ASN B ** 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 = 0.4130 r_free = 0.4130 target = 0.168755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.142353 restraints weight = 29587.994| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 1.53 r_work: 0.3600 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16567 Z= 0.137 Angle : 0.623 12.368 22565 Z= 0.311 Chirality : 0.041 0.343 2707 Planarity : 0.005 0.069 2790 Dihedral : 5.313 57.723 2350 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 6.62 % Allowed : 25.76 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 aren not related in a simple way. whole: 0.24 (0.19), residues: 2133 helix: 1.08 (0.14), residues: 1526 sheet: -0.07 (1.49), residues: 13 loop : -2.31 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Z 31 TYR 0.018 0.001 TYR B 44 PHE 0.017 0.001 PHE F 226 TRP 0.037 0.001 TRP F 201 HIS 0.004 0.001 HIS Y 145 Details of bonding type rmsd covalent geometry : bond 0.00319 (16567) covalent geometry : angle 0.62287 (22565) hydrogen bonds : bond 0.03882 ( 1040) hydrogen bonds : angle 4.19509 ( 3114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 138 time to evaluate : 0.521 Fit side-chains REVERT: Y 39 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.7979 (mp) REVERT: Y 147 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8118 (mt) REVERT: Z 49 TYR cc_start: 0.7090 (OUTLIER) cc_final: 0.5969 (p90) REVERT: E 25 ASP cc_start: 0.7123 (t70) cc_final: 0.6640 (t0) REVERT: E 107 LEU cc_start: 0.7563 (mm) cc_final: 0.7094 (mt) REVERT: E 120 MET cc_start: 0.6210 (OUTLIER) cc_final: 0.5603 (mtt) REVERT: E 142 GLU cc_start: 0.4593 (OUTLIER) cc_final: 0.3391 (mp0) REVERT: E 175 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6517 (mt) REVERT: E 205 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7243 (ptp) REVERT: F 49 TYR cc_start: 0.7873 (OUTLIER) cc_final: 0.5967 (p90) outliers start: 61 outliers final: 44 residues processed: 183 average time/residue: 0.4973 time to fit residues: 103.3098 Evaluate side-chains 182 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 130 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Y residue 45 HIS Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 147 ILE Chi-restraints excluded: chain Y residue 166 ILE Chi-restraints excluded: chain Y residue 181 VAL Chi-restraints excluded: chain Y residue 229 ILE Chi-restraints excluded: chain Y residue 234 LEU Chi-restraints excluded: chain Z residue 34 ASN Chi-restraints excluded: chain Z residue 42 ILE Chi-restraints excluded: chain Z residue 49 TYR Chi-restraints excluded: chain Z residue 105 MET Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain Z residue 214 SER Chi-restraints excluded: chain Z residue 216 ILE Chi-restraints excluded: chain Z residue 288 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 45 HIS Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 118 TRP Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 165 LYS Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 228 LYS Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 306 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 4 optimal weight: 0.0870 chunk 14 optimal weight: 0.8980 chunk 169 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 164 optimal weight: 0.9980 chunk 111 optimal weight: 0.2980 chunk 19 optimal weight: 2.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 128 GLN ** Z 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 ASN ** C 57 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 ASN B ** 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 = 0.4142 r_free = 0.4142 target = 0.169764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.144084 restraints weight = 28557.777| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 1.66 r_work: 0.3624 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3518 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3518 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16567 Z= 0.121 Angle : 0.608 12.895 22565 Z= 0.303 Chirality : 0.041 0.344 2707 Planarity : 0.005 0.069 2790 Dihedral : 5.223 59.436 2350 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 5.96 % Allowed : 26.89 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 aren not related in a simple way. whole: 0.36 (0.19), residues: 2133 helix: 1.18 (0.14), residues: 1528 sheet: -0.01 (1.50), residues: 13 loop : -2.30 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Y 131 TYR 0.019 0.001 TYR B 44 PHE 0.015 0.001 PHE F 226 TRP 0.040 0.001 TRP F 201 HIS 0.003 0.001 HIS Z 62 Details of bonding type rmsd covalent geometry : bond 0.00273 (16567) covalent geometry : angle 0.60750 (22565) hydrogen bonds : bond 0.03633 ( 1040) hydrogen bonds : angle 4.09685 ( 3114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 133 time to evaluate : 0.495 Fit side-chains REVERT: Y 39 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.7978 (mp) REVERT: Y 147 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8126 (mt) REVERT: Z 49 TYR cc_start: 0.7173 (OUTLIER) cc_final: 0.6008 (p90) REVERT: E 142 GLU cc_start: 0.4507 (OUTLIER) cc_final: 0.3366 (mp0) REVERT: E 175 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6473 (mt) REVERT: E 205 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7322 (ptp) REVERT: F 49 TYR cc_start: 0.7838 (OUTLIER) cc_final: 0.5962 (p90) outliers start: 50 outliers final: 41 residues processed: 170 average time/residue: 0.5088 time to fit residues: 97.5029 Evaluate side-chains 174 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 126 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 39 ILE Chi-restraints excluded: chain Y residue 45 HIS Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 147 ILE Chi-restraints excluded: chain Y residue 166 ILE Chi-restraints excluded: chain Y residue 181 VAL Chi-restraints excluded: chain Y residue 231 THR Chi-restraints excluded: chain Y residue 234 LEU Chi-restraints excluded: chain Z residue 34 ASN Chi-restraints excluded: chain Z residue 42 ILE Chi-restraints excluded: chain Z residue 49 TYR Chi-restraints excluded: chain Z residue 105 MET Chi-restraints excluded: chain Z residue 214 SER Chi-restraints excluded: chain Z residue 216 ILE Chi-restraints excluded: chain Z residue 288 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 45 HIS Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 142 GLU Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 17 MET Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 118 TRP Chi-restraints excluded: chain F residue 139 ILE Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 265 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 140 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 26 optimal weight: 0.0470 chunk 61 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 144 optimal weight: 0.0370 chunk 44 optimal weight: 3.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 128 GLN Y 203 ASN ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 ASN F 263 GLN ** C 57 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.168697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.141360 restraints weight = 29981.509| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.84 r_work: 0.3612 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3497 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16567 Z= 0.129 Angle : 0.614 12.809 22565 Z= 0.307 Chirality : 0.041 0.341 2707 Planarity : 0.005 0.070 2790 Dihedral : 5.224 58.433 2350 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 6.08 % Allowed : 26.89 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 aren not related in a simple way. whole: 0.36 (0.19), residues: 2133 helix: 1.18 (0.14), residues: 1525 sheet: -0.02 (1.50), residues: 13 loop : -2.28 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 61 TYR 0.016 0.001 TYR B 44 PHE 0.015 0.001 PHE F 226 TRP 0.047 0.001 TRP F 201 HIS 0.004 0.001 HIS Y 145 Details of bonding type rmsd covalent geometry : bond 0.00295 (16567) covalent geometry : angle 0.61402 (22565) hydrogen bonds : bond 0.03726 ( 1040) hydrogen bonds : angle 4.11493 ( 3114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6320.53 seconds wall clock time: 108 minutes 4.45 seconds (6484.45 seconds total)