Starting phenix.real_space_refine on Wed Mar 4 21:50:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u6d_20663/03_2026/6u6d_20663.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u6d_20663/03_2026/6u6d_20663.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6u6d_20663/03_2026/6u6d_20663.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u6d_20663/03_2026/6u6d_20663.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6u6d_20663/03_2026/6u6d_20663.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u6d_20663/03_2026/6u6d_20663.map" } resolution = 3.6 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 2 8.98 5 S 68 5.16 5 C 10564 2.51 5 N 2896 2.21 5 O 3240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16770 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2467 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "C" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2467 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "E" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2467 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "G" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2467 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "B" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "D" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "F" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "H" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.87, per 1000 atoms: 0.23 Number of scatterers: 16770 At special positions: 0 Unit cell: (149.319, 149.319, 116.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 2 19.00 S 68 16.00 O 3240 8.00 N 2896 7.00 C 10564 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: 1.43 Conformation dependent library (CDL) restraints added in 762.7 milliseconds 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3952 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 16 sheets defined 48.1% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 21 through 43 removed outlier: 4.022A pdb=" N LEU A 25 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 69 through 105 removed outlier: 4.556A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 156 removed outlier: 3.704A pdb=" N LYS A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 171 removed outlier: 3.658A pdb=" N GLU A 171 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.509A pdb=" N GLY A 177 " --> pdb=" O ASN A 174 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA A 178 " --> pdb=" O VAL A 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 174 through 178' Processing helix chain 'A' and resid 187 through 202 removed outlier: 3.786A pdb=" N THR A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 224 removed outlier: 3.628A pdb=" N GLY A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 240 removed outlier: 3.704A pdb=" N SER A 240 " --> pdb=" O GLY A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 257 Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 323 through 334 removed outlier: 3.810A pdb=" N GLU A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 43 removed outlier: 4.022A pdb=" N LEU C 25 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA C 36 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 57 Processing helix chain 'C' and resid 69 through 105 removed outlier: 4.555A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR C 78 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL C 91 " --> pdb=" O PHE C 87 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU C 92 " --> pdb=" O ALA C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 156 removed outlier: 3.703A pdb=" N LYS C 150 " --> pdb=" O GLU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 171 removed outlier: 3.659A pdb=" N GLU C 171 " --> pdb=" O VAL C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 178 removed outlier: 3.510A pdb=" N GLY C 177 " --> pdb=" O ASN C 174 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA C 178 " --> pdb=" O VAL C 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 174 through 178' Processing helix chain 'C' and resid 187 through 202 removed outlier: 3.785A pdb=" N THR C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 216 through 224 removed outlier: 3.627A pdb=" N GLY C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 240 removed outlier: 3.705A pdb=" N SER C 240 " --> pdb=" O GLY C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 257 Processing helix chain 'C' and resid 279 through 284 Processing helix chain 'C' and resid 284 through 290 Processing helix chain 'C' and resid 323 through 334 removed outlier: 3.810A pdb=" N GLU C 328 " --> pdb=" O PRO C 324 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 43 removed outlier: 4.023A pdb=" N LEU E 25 " --> pdb=" O THR E 21 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA E 36 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE E 41 " --> pdb=" O GLY E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 69 through 105 removed outlier: 4.556A pdb=" N VAL E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR E 78 " --> pdb=" O TYR E 74 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL E 91 " --> pdb=" O PHE E 87 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 156 removed outlier: 3.704A pdb=" N LYS E 150 " --> pdb=" O GLU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 171 removed outlier: 3.659A pdb=" N GLU E 171 " --> pdb=" O VAL E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 178 removed outlier: 3.510A pdb=" N GLY E 177 " --> pdb=" O ASN E 174 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA E 178 " --> pdb=" O VAL E 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 174 through 178' Processing helix chain 'E' and resid 187 through 202 removed outlier: 3.785A pdb=" N THR E 191 " --> pdb=" O SER E 187 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.628A pdb=" N GLY E 224 " --> pdb=" O LEU E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 240 removed outlier: 3.705A pdb=" N SER E 240 " --> pdb=" O GLY E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 257 Processing helix chain 'E' and resid 279 through 284 Processing helix chain 'E' and resid 284 through 290 Processing helix chain 'E' and resid 323 through 334 removed outlier: 3.810A pdb=" N GLU E 328 " --> pdb=" O PRO E 324 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR E 333 " --> pdb=" O ARG E 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 43 removed outlier: 4.023A pdb=" N LEU G 25 " --> pdb=" O THR G 21 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA G 36 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE G 41 " --> pdb=" O GLY G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 57 Processing helix chain 'G' and resid 69 through 105 removed outlier: 4.555A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR G 78 " --> pdb=" O TYR G 74 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL G 91 " --> pdb=" O PHE G 87 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU G 92 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 156 removed outlier: 3.704A pdb=" N LYS G 150 " --> pdb=" O GLU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 171 removed outlier: 3.659A pdb=" N GLU G 171 " --> pdb=" O VAL G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 178 removed outlier: 3.510A pdb=" N GLY G 177 " --> pdb=" O ASN G 174 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA G 178 " --> pdb=" O VAL G 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 174 through 178' Processing helix chain 'G' and resid 187 through 202 removed outlier: 3.786A pdb=" N THR G 191 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 215 No H-bonds generated for 'chain 'G' and resid 213 through 215' Processing helix chain 'G' and resid 216 through 224 removed outlier: 3.628A pdb=" N GLY G 224 " --> pdb=" O LEU G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 240 removed outlier: 3.706A pdb=" N SER G 240 " --> pdb=" O GLY G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 257 Processing helix chain 'G' and resid 279 through 284 Processing helix chain 'G' and resid 284 through 290 Processing helix chain 'G' and resid 323 through 334 removed outlier: 3.809A pdb=" N GLU G 328 " --> pdb=" O PRO G 324 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR G 333 " --> pdb=" O ARG G 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 131 Processing helix chain 'B' and resid 146 through 155 removed outlier: 4.266A pdb=" N LYS B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS B 151 " --> pdb=" O ASN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 171 removed outlier: 3.680A pdb=" N GLU B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 202 Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.748A pdb=" N GLY B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 242 removed outlier: 3.694A pdb=" N ILE B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER B 242 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 256 Processing helix chain 'B' and resid 284 through 289 removed outlier: 3.581A pdb=" N VAL B 288 " --> pdb=" O ASP B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 334 removed outlier: 3.990A pdb=" N GLU B 328 " --> pdb=" O PRO B 324 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 131 Processing helix chain 'D' and resid 146 through 155 removed outlier: 4.266A pdb=" N LYS D 150 " --> pdb=" O GLU D 146 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS D 151 " --> pdb=" O ASN D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 171 removed outlier: 3.681A pdb=" N GLU D 171 " --> pdb=" O VAL D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 202 Processing helix chain 'D' and resid 216 through 224 removed outlier: 3.748A pdb=" N GLY D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 242 removed outlier: 3.695A pdb=" N ILE D 234 " --> pdb=" O SER D 230 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER D 240 " --> pdb=" O GLY D 236 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER D 242 " --> pdb=" O LEU D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 256 Processing helix chain 'D' and resid 284 through 289 removed outlier: 3.580A pdb=" N VAL D 288 " --> pdb=" O ASP D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 334 removed outlier: 3.989A pdb=" N GLU D 328 " --> pdb=" O PRO D 324 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 131 Processing helix chain 'F' and resid 146 through 155 removed outlier: 4.266A pdb=" N LYS F 150 " --> pdb=" O GLU F 146 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS F 151 " --> pdb=" O ASN F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 171 removed outlier: 3.681A pdb=" N GLU F 171 " --> pdb=" O VAL F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 202 Processing helix chain 'F' and resid 216 through 224 removed outlier: 3.748A pdb=" N GLY F 224 " --> pdb=" O LEU F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 242 removed outlier: 3.694A pdb=" N ILE F 234 " --> pdb=" O SER F 230 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER F 240 " --> pdb=" O GLY F 236 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER F 242 " --> pdb=" O LEU F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 256 Processing helix chain 'F' and resid 284 through 289 removed outlier: 3.580A pdb=" N VAL F 288 " --> pdb=" O ASP F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 334 removed outlier: 3.990A pdb=" N GLU F 328 " --> pdb=" O PRO F 324 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG F 329 " --> pdb=" O GLU F 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 131 Processing helix chain 'H' and resid 146 through 155 removed outlier: 4.266A pdb=" N LYS H 150 " --> pdb=" O GLU H 146 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS H 151 " --> pdb=" O ASN H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 171 removed outlier: 3.682A pdb=" N GLU H 171 " --> pdb=" O VAL H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 202 Processing helix chain 'H' and resid 216 through 224 removed outlier: 3.748A pdb=" N GLY H 224 " --> pdb=" O LEU H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 242 removed outlier: 3.693A pdb=" N ILE H 234 " --> pdb=" O SER H 230 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER H 240 " --> pdb=" O GLY H 236 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER H 242 " --> pdb=" O LEU H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 256 Processing helix chain 'H' and resid 284 through 289 removed outlier: 3.581A pdb=" N VAL H 288 " --> pdb=" O ASP H 284 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 334 removed outlier: 3.989A pdb=" N GLU H 328 " --> pdb=" O PRO H 324 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG H 329 " --> pdb=" O GLU H 325 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 159 removed outlier: 3.587A pdb=" N ASN A 158 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A 118 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU A 142 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE A 120 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 119 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 264 through 268 removed outlier: 3.767A pdb=" N ILE A 317 " --> pdb=" O GLY A 297 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE A 321 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE A 293 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 158 through 159 removed outlier: 3.586A pdb=" N ASN C 158 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C 118 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LEU C 142 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE C 120 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL C 119 " --> pdb=" O ILE C 182 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 264 through 268 removed outlier: 3.767A pdb=" N ILE C 317 " --> pdb=" O GLY C 297 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE C 321 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE C 293 " --> pdb=" O ILE C 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 158 through 159 removed outlier: 3.587A pdb=" N ASN E 158 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL E 118 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU E 142 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE E 120 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL E 119 " --> pdb=" O ILE E 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 264 through 268 removed outlier: 3.767A pdb=" N ILE E 317 " --> pdb=" O GLY E 297 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE E 321 " --> pdb=" O ILE E 293 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE E 293 " --> pdb=" O ILE E 321 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 158 through 159 removed outlier: 3.587A pdb=" N ASN G 158 " --> pdb=" O VAL G 139 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL G 118 " --> pdb=" O PHE G 140 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU G 142 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE G 120 " --> pdb=" O LEU G 142 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL G 119 " --> pdb=" O ILE G 182 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 264 through 268 removed outlier: 3.767A pdb=" N ILE G 317 " --> pdb=" O GLY G 297 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE G 321 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE G 293 " --> pdb=" O ILE G 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 158 through 161 removed outlier: 6.405A pdb=" N VAL B 139 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL B 160 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL B 141 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL B 118 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU B 142 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE B 120 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL B 119 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN B 227 " --> pdb=" O ILE B 207 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 263 through 268 removed outlier: 3.902A pdb=" N GLY B 295 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE B 321 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE B 293 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 158 through 161 removed outlier: 6.404A pdb=" N VAL D 139 " --> pdb=" O ASN D 158 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL D 160 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL D 141 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL D 118 " --> pdb=" O PHE D 140 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU D 142 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE D 120 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL D 119 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN D 227 " --> pdb=" O ILE D 207 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 263 through 268 removed outlier: 3.903A pdb=" N GLY D 295 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE D 321 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE D 293 " --> pdb=" O ILE D 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 158 through 161 removed outlier: 6.405A pdb=" N VAL F 139 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL F 160 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL F 141 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL F 118 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU F 142 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE F 120 " --> pdb=" O LEU F 142 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL F 119 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN F 227 " --> pdb=" O ILE F 207 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 263 through 268 removed outlier: 3.903A pdb=" N GLY F 295 " --> pdb=" O LEU F 319 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE F 321 " --> pdb=" O ILE F 293 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE F 293 " --> pdb=" O ILE F 321 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 158 through 161 removed outlier: 6.405A pdb=" N VAL H 139 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL H 160 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL H 141 " --> pdb=" O VAL H 160 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL H 118 " --> pdb=" O PHE H 140 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU H 142 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE H 120 " --> pdb=" O LEU H 142 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL H 119 " --> pdb=" O ILE H 182 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN H 227 " --> pdb=" O ILE H 207 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 263 through 268 removed outlier: 3.902A pdb=" N GLY H 295 " --> pdb=" O LEU H 319 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE H 321 " --> pdb=" O ILE H 293 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE H 293 " --> pdb=" O ILE H 321 " (cutoff:3.500A) 692 hydrogen bonds defined for protein. 2040 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: 2.97 Time building geometry restraints manager: 1.90 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: 5756 1.34 - 1.46: 3260 1.46 - 1.58: 7880 1.58 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 17008 Sorted by residual: bond pdb=" C VAL B 267 " pdb=" O VAL B 267 " ideal model delta sigma weight residual 1.232 1.240 -0.008 8.90e-03 1.26e+04 7.32e-01 bond pdb=" CA SER G 240 " pdb=" CB SER G 240 " ideal model delta sigma weight residual 1.532 1.517 0.015 1.79e-02 3.12e+03 6.94e-01 bond pdb=" C VAL H 267 " pdb=" O VAL H 267 " ideal model delta sigma weight residual 1.232 1.240 -0.007 8.90e-03 1.26e+04 6.93e-01 bond pdb=" CA SER A 240 " pdb=" CB SER A 240 " ideal model delta sigma weight residual 1.532 1.518 0.014 1.79e-02 3.12e+03 6.43e-01 bond pdb=" CA SER C 240 " pdb=" CB SER C 240 " ideal model delta sigma weight residual 1.532 1.518 0.014 1.79e-02 3.12e+03 6.43e-01 ... (remaining 17003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 22450 1.36 - 2.73: 470 2.73 - 4.09: 76 4.09 - 5.46: 4 5.46 - 6.82: 8 Bond angle restraints: 23008 Sorted by residual: angle pdb=" N ILE D 334 " pdb=" CA ILE D 334 " pdb=" C ILE D 334 " ideal model delta sigma weight residual 111.91 109.33 2.58 8.90e-01 1.26e+00 8.42e+00 angle pdb=" N ILE F 334 " pdb=" CA ILE F 334 " pdb=" C ILE F 334 " ideal model delta sigma weight residual 111.91 109.35 2.56 8.90e-01 1.26e+00 8.25e+00 angle pdb=" N ILE B 334 " pdb=" CA ILE B 334 " pdb=" C ILE B 334 " ideal model delta sigma weight residual 111.91 109.35 2.56 8.90e-01 1.26e+00 8.24e+00 angle pdb=" N ILE H 334 " pdb=" CA ILE H 334 " pdb=" C ILE H 334 " ideal model delta sigma weight residual 111.91 109.38 2.53 8.90e-01 1.26e+00 8.11e+00 angle pdb=" C SER E 273 " pdb=" N LYS E 274 " pdb=" CA LYS E 274 " ideal model delta sigma weight residual 121.54 125.38 -3.84 1.91e+00 2.74e-01 4.05e+00 ... (remaining 23003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.14: 8990 14.14 - 28.28: 982 28.28 - 42.42: 300 42.42 - 56.55: 52 56.55 - 70.69: 12 Dihedral angle restraints: 10336 sinusoidal: 4184 harmonic: 6152 Sorted by residual: dihedral pdb=" CA GLU B 133 " pdb=" C GLU B 133 " pdb=" N LEU B 134 " pdb=" CA LEU B 134 " ideal model delta harmonic sigma weight residual 180.00 163.70 16.30 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA GLU D 133 " pdb=" C GLU D 133 " pdb=" N LEU D 134 " pdb=" CA LEU D 134 " ideal model delta harmonic sigma weight residual 180.00 163.70 16.30 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA GLU H 133 " pdb=" C GLU H 133 " pdb=" N LEU H 134 " pdb=" CA LEU H 134 " ideal model delta harmonic sigma weight residual 180.00 163.76 16.24 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 10333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1357 0.027 - 0.054: 813 0.054 - 0.081: 281 0.081 - 0.109: 173 0.109 - 0.136: 64 Chirality restraints: 2688 Sorted by residual: chirality pdb=" CA ILE A 321 " pdb=" N ILE A 321 " pdb=" C ILE A 321 " pdb=" CB ILE A 321 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA ILE G 321 " pdb=" N ILE G 321 " pdb=" C ILE G 321 " pdb=" CB ILE G 321 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA ILE D 321 " pdb=" N ILE D 321 " pdb=" C ILE D 321 " pdb=" CB ILE D 321 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 2685 not shown) Planarity restraints: 2988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL H 175 " 0.005 2.00e-02 2.50e+03 9.42e-03 8.87e-01 pdb=" C VAL H 175 " -0.016 2.00e-02 2.50e+03 pdb=" O VAL H 175 " 0.006 2.00e-02 2.50e+03 pdb=" N ARG H 176 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 175 " 0.005 2.00e-02 2.50e+03 9.31e-03 8.66e-01 pdb=" C VAL B 175 " -0.016 2.00e-02 2.50e+03 pdb=" O VAL B 175 " 0.006 2.00e-02 2.50e+03 pdb=" N ARG B 176 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 175 " 0.005 2.00e-02 2.50e+03 9.30e-03 8.66e-01 pdb=" C VAL D 175 " -0.016 2.00e-02 2.50e+03 pdb=" O VAL D 175 " 0.006 2.00e-02 2.50e+03 pdb=" N ARG D 176 " 0.005 2.00e-02 2.50e+03 ... (remaining 2985 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.81: 4613 2.81 - 3.39: 17415 3.39 - 3.97: 29760 3.97 - 4.56: 41610 4.56 - 5.14: 65136 Nonbonded interactions: 158534 Sorted by model distance: nonbonded pdb=" O ILE F 285 " pdb=" OG1 THR F 289 " model vdw 2.227 3.040 nonbonded pdb=" O ILE B 285 " pdb=" OG1 THR B 289 " model vdw 2.227 3.040 nonbonded pdb=" O ILE H 285 " pdb=" OG1 THR H 289 " model vdw 2.227 3.040 nonbonded pdb=" O ILE D 285 " pdb=" OG1 THR D 289 " model vdw 2.227 3.040 nonbonded pdb=" OE1 GLU E 133 " pdb=" OG SER F 240 " model vdw 2.230 3.040 ... (remaining 158529 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 16.500 Find NCS groups from input model: 0.120 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 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 : 0.002 0.019 17008 Z= 0.123 Angle : 0.509 6.822 23008 Z= 0.313 Chirality : 0.044 0.136 2688 Planarity : 0.002 0.019 2988 Dihedral : 12.889 70.693 6384 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % 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 are not related in a simple way. whole: -4.06 (0.14), residues: 2140 helix: -2.13 (0.14), residues: 988 sheet: -2.70 (0.22), residues: 356 loop : -3.22 (0.16), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 308 TYR 0.010 0.001 TYR G 33 PHE 0.004 0.001 PHE G 75 TRP 0.003 0.001 TRP G 46 HIS 0.002 0.000 HIS A 286 Details of bonding type rmsd covalent geometry : bond 0.00240 (17008) covalent geometry : angle 0.50888 (23008) hydrogen bonds : bond 0.17568 ( 692) hydrogen bonds : angle 7.03016 ( 2040) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 0.581 Fit side-chains REVERT: A 33 TYR cc_start: 0.8087 (t80) cc_final: 0.7849 (t80) REVERT: A 103 GLN cc_start: 0.7601 (tp40) cc_final: 0.7346 (tp-100) REVERT: A 146 GLU cc_start: 0.8126 (tp30) cc_final: 0.7897 (tp30) REVERT: A 250 MET cc_start: 0.8435 (mtp) cc_final: 0.8221 (mtp) REVERT: A 281 LEU cc_start: 0.8491 (mt) cc_final: 0.8002 (pp) REVERT: C 146 GLU cc_start: 0.8122 (tp30) cc_final: 0.7807 (tp30) REVERT: C 250 MET cc_start: 0.8431 (mtp) cc_final: 0.8204 (mtp) REVERT: C 281 LEU cc_start: 0.8516 (mt) cc_final: 0.7983 (pp) REVERT: E 96 GLU cc_start: 0.7766 (tt0) cc_final: 0.7560 (tt0) REVERT: E 146 GLU cc_start: 0.8102 (tp30) cc_final: 0.7781 (tp30) REVERT: E 250 MET cc_start: 0.8357 (mtp) cc_final: 0.8115 (mtp) REVERT: E 281 LEU cc_start: 0.8499 (mt) cc_final: 0.8016 (pp) REVERT: G 146 GLU cc_start: 0.8115 (tp30) cc_final: 0.7797 (tp30) REVERT: G 250 MET cc_start: 0.8392 (mtp) cc_final: 0.8168 (mtp) REVERT: G 281 LEU cc_start: 0.8517 (mt) cc_final: 0.8081 (pp) REVERT: B 250 MET cc_start: 0.7966 (mtt) cc_final: 0.7601 (ttm) REVERT: D 250 MET cc_start: 0.7826 (mtt) cc_final: 0.7393 (ttm) REVERT: F 250 MET cc_start: 0.7959 (mtt) cc_final: 0.7553 (ttm) outliers start: 0 outliers final: 0 residues processed: 344 average time/residue: 0.1742 time to fit residues: 83.2728 Evaluate side-chains 248 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 158 ASN C 39 HIS E 39 HIS E 158 ASN E 174 ASN G 39 HIS G 158 ASN B 161 HIS D 161 HIS F 161 HIS H 161 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.123766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.097886 restraints weight = 22455.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.099483 restraints weight = 17406.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.100571 restraints weight = 14347.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.101225 restraints weight = 12453.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.101823 restraints weight = 11317.090| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17008 Z= 0.181 Angle : 0.511 6.968 23008 Z= 0.270 Chirality : 0.047 0.138 2688 Planarity : 0.004 0.043 2988 Dihedral : 3.897 16.563 2380 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.96 % Allowed : 11.44 % Favored : 86.60 % 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 are not related in a simple way. whole: -2.98 (0.16), residues: 2140 helix: -1.07 (0.16), residues: 976 sheet: -2.48 (0.23), residues: 332 loop : -2.75 (0.16), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 298 TYR 0.018 0.001 TYR E 51 PHE 0.009 0.001 PHE B 251 TRP 0.005 0.001 TRP A 123 HIS 0.003 0.001 HIS E 117 Details of bonding type rmsd covalent geometry : bond 0.00439 (17008) covalent geometry : angle 0.51139 (23008) hydrogen bonds : bond 0.04043 ( 692) hydrogen bonds : angle 5.30930 ( 2040) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 260 time to evaluate : 0.628 Fit side-chains REVERT: A 281 LEU cc_start: 0.8475 (mt) cc_final: 0.8022 (pp) REVERT: C 281 LEU cc_start: 0.8496 (mt) cc_final: 0.8008 (pp) REVERT: E 281 LEU cc_start: 0.8481 (mt) cc_final: 0.8024 (pp) REVERT: G 281 LEU cc_start: 0.8479 (mt) cc_final: 0.8023 (pp) REVERT: D 250 MET cc_start: 0.7961 (mtt) cc_final: 0.7738 (ttm) outliers start: 36 outliers final: 25 residues processed: 283 average time/residue: 0.1502 time to fit residues: 62.0626 Evaluate side-chains 260 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 235 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 228 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 75 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 122 optimal weight: 0.3980 chunk 45 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 190 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN C 158 ASN C 219 GLN E 219 GLN G 219 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.126834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.102496 restraints weight = 22265.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.102992 restraints weight = 20813.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.103454 restraints weight = 18793.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.103707 restraints weight = 15378.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.104837 restraints weight = 14108.041| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 17008 Z= 0.101 Angle : 0.436 6.863 23008 Z= 0.231 Chirality : 0.045 0.148 2688 Planarity : 0.003 0.032 2988 Dihedral : 3.589 12.895 2380 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.47 % Allowed : 13.51 % Favored : 85.02 % 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 are not related in a simple way. whole: -2.28 (0.16), residues: 2140 helix: -0.47 (0.16), residues: 1000 sheet: -1.98 (0.25), residues: 332 loop : -2.56 (0.17), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 308 TYR 0.019 0.001 TYR A 65 PHE 0.005 0.001 PHE A 75 TRP 0.003 0.001 TRP E 46 HIS 0.003 0.001 HIS G 39 Details of bonding type rmsd covalent geometry : bond 0.00235 (17008) covalent geometry : angle 0.43552 (23008) hydrogen bonds : bond 0.03034 ( 692) hydrogen bonds : angle 4.82137 ( 2040) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 242 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 LEU cc_start: 0.8473 (mt) cc_final: 0.7936 (pp) REVERT: C 103 GLN cc_start: 0.7855 (tp-100) cc_final: 0.7646 (tp-100) REVERT: C 281 LEU cc_start: 0.8497 (mt) cc_final: 0.7933 (pp) REVERT: C 326 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7383 (mm-30) REVERT: E 281 LEU cc_start: 0.8472 (mt) cc_final: 0.7929 (pp) REVERT: E 326 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7498 (mm-30) REVERT: G 103 GLN cc_start: 0.7861 (tp-100) cc_final: 0.7658 (tp-100) REVERT: G 281 LEU cc_start: 0.8478 (mt) cc_final: 0.7939 (pp) outliers start: 27 outliers final: 22 residues processed: 254 average time/residue: 0.1428 time to fit residues: 53.2216 Evaluate side-chains 244 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 222 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 264 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 84 optimal weight: 0.1980 chunk 91 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 chunk 83 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 118 optimal weight: 0.0970 chunk 119 optimal weight: 1.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.147411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.124593 restraints weight = 21025.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.126250 restraints weight = 15560.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.127445 restraints weight = 12336.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.128114 restraints weight = 10521.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.128679 restraints weight = 9435.112| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 17008 Z= 0.085 Angle : 0.415 6.362 23008 Z= 0.220 Chirality : 0.045 0.152 2688 Planarity : 0.003 0.036 2988 Dihedral : 3.354 12.046 2380 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.63 % Allowed : 15.03 % Favored : 83.33 % 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 are not related in a simple way. whole: -1.57 (0.17), residues: 2140 helix: 0.17 (0.17), residues: 976 sheet: -1.53 (0.27), residues: 332 loop : -2.27 (0.17), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 93 TYR 0.018 0.001 TYR G 51 PHE 0.008 0.000 PHE G 75 TRP 0.002 0.000 TRP E 52 HIS 0.003 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00193 (17008) covalent geometry : angle 0.41475 (23008) hydrogen bonds : bond 0.02650 ( 692) hydrogen bonds : angle 4.50725 ( 2040) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 239 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.7858 (tp-100) cc_final: 0.7486 (tp-100) REVERT: A 281 LEU cc_start: 0.8493 (mt) cc_final: 0.8008 (pp) REVERT: A 326 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7439 (mm-30) REVERT: C 281 LEU cc_start: 0.8499 (mt) cc_final: 0.7933 (pp) REVERT: C 326 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7498 (mm-30) REVERT: E 281 LEU cc_start: 0.8497 (mt) cc_final: 0.7971 (pp) REVERT: E 326 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7555 (mm-30) REVERT: G 75 PHE cc_start: 0.8413 (t80) cc_final: 0.8183 (t80) REVERT: G 281 LEU cc_start: 0.8418 (mt) cc_final: 0.8005 (pp) REVERT: G 326 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7512 (mm-30) REVERT: B 132 ARG cc_start: 0.7847 (mtm-85) cc_final: 0.7623 (mtm-85) REVERT: F 132 ARG cc_start: 0.7862 (mtm-85) cc_final: 0.7620 (mtm-85) REVERT: H 132 ARG cc_start: 0.7856 (mtm-85) cc_final: 0.7553 (mtm-85) outliers start: 30 outliers final: 20 residues processed: 257 average time/residue: 0.1507 time to fit residues: 56.1166 Evaluate side-chains 245 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 225 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 87 PHE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 228 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 196 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 40 optimal weight: 0.0010 chunk 162 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 42 optimal weight: 0.4980 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.127852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.104603 restraints weight = 22072.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.104270 restraints weight = 15811.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.104532 restraints weight = 13105.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.104620 restraints weight = 12359.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.104797 restraints weight = 11913.810| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17008 Z= 0.110 Angle : 0.424 6.509 23008 Z= 0.224 Chirality : 0.045 0.146 2688 Planarity : 0.003 0.027 2988 Dihedral : 3.367 11.714 2380 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.91 % Allowed : 15.74 % Favored : 82.35 % 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 are not related in a simple way. whole: -1.28 (0.17), residues: 2140 helix: 0.38 (0.17), residues: 976 sheet: -1.31 (0.27), residues: 332 loop : -2.11 (0.18), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 308 TYR 0.022 0.001 TYR C 51 PHE 0.005 0.001 PHE A 75 TRP 0.003 0.000 TRP C 123 HIS 0.005 0.001 HIS C 286 Details of bonding type rmsd covalent geometry : bond 0.00261 (17008) covalent geometry : angle 0.42436 (23008) hydrogen bonds : bond 0.02831 ( 692) hydrogen bonds : angle 4.49451 ( 2040) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 235 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.7907 (tp-100) cc_final: 0.7597 (tp-100) REVERT: A 281 LEU cc_start: 0.8517 (mt) cc_final: 0.8027 (pp) REVERT: C 281 LEU cc_start: 0.8514 (mt) cc_final: 0.7951 (pp) REVERT: E 281 LEU cc_start: 0.8530 (mt) cc_final: 0.7994 (pp) REVERT: G 103 GLN cc_start: 0.7873 (tp-100) cc_final: 0.7601 (tp-100) REVERT: G 281 LEU cc_start: 0.8490 (mt) cc_final: 0.8057 (pp) REVERT: B 132 ARG cc_start: 0.7881 (mtm-85) cc_final: 0.7678 (mtm-85) REVERT: F 132 ARG cc_start: 0.7904 (mtm-85) cc_final: 0.7683 (mtm-85) outliers start: 35 outliers final: 30 residues processed: 256 average time/residue: 0.1402 time to fit residues: 52.2527 Evaluate side-chains 258 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 228 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 105 LYS Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain F residue 281 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 139 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 58 optimal weight: 0.4980 chunk 115 optimal weight: 0.6980 chunk 168 optimal weight: 0.4980 chunk 170 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 286 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.146522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.122992 restraints weight = 20862.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.124863 restraints weight = 15033.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.126115 restraints weight = 11826.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.126919 restraints weight = 9959.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.127333 restraints weight = 8838.091| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17008 Z= 0.097 Angle : 0.419 9.365 23008 Z= 0.220 Chirality : 0.045 0.146 2688 Planarity : 0.003 0.037 2988 Dihedral : 3.302 11.698 2380 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.07 % Allowed : 16.01 % Favored : 81.92 % 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 are not related in a simple way. whole: -1.03 (0.17), residues: 2140 helix: 0.54 (0.17), residues: 980 sheet: -1.18 (0.27), residues: 332 loop : -1.93 (0.18), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 308 TYR 0.020 0.001 TYR C 51 PHE 0.017 0.001 PHE A 75 TRP 0.002 0.000 TRP A 46 HIS 0.004 0.001 HIS G 286 Details of bonding type rmsd covalent geometry : bond 0.00229 (17008) covalent geometry : angle 0.41913 (23008) hydrogen bonds : bond 0.02667 ( 692) hydrogen bonds : angle 4.39509 ( 2040) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 234 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.7868 (tp-100) cc_final: 0.7568 (tp-100) REVERT: A 281 LEU cc_start: 0.8420 (mt) cc_final: 0.8009 (pp) REVERT: A 326 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7392 (mm-30) REVERT: C 281 LEU cc_start: 0.8502 (mt) cc_final: 0.7951 (pp) REVERT: C 326 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7380 (mm-30) REVERT: E 281 LEU cc_start: 0.8436 (mt) cc_final: 0.7982 (pp) REVERT: E 326 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7380 (mm-30) REVERT: G 103 GLN cc_start: 0.7876 (tp-100) cc_final: 0.7611 (tp-100) REVERT: G 281 LEU cc_start: 0.8435 (mt) cc_final: 0.8017 (pp) REVERT: G 326 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7377 (mm-30) REVERT: B 132 ARG cc_start: 0.7834 (mtm-85) cc_final: 0.7584 (mtm-85) REVERT: F 132 ARG cc_start: 0.7846 (mtm-85) cc_final: 0.7637 (mtm-85) outliers start: 38 outliers final: 33 residues processed: 260 average time/residue: 0.1428 time to fit residues: 54.3249 Evaluate side-chains 259 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 226 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 105 LYS Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain H residue 189 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 186 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 171 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 105 optimal weight: 0.8980 chunk 130 optimal weight: 0.0370 chunk 201 optimal weight: 0.2980 chunk 133 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 146 optimal weight: 0.5980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 103 GLN G 286 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.129700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.105353 restraints weight = 21848.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.105502 restraints weight = 15908.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.106388 restraints weight = 12847.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.106892 restraints weight = 11376.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.107031 restraints weight = 10632.686| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17008 Z= 0.086 Angle : 0.411 10.126 23008 Z= 0.215 Chirality : 0.045 0.149 2688 Planarity : 0.003 0.023 2988 Dihedral : 3.229 12.220 2380 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.40 % Allowed : 16.56 % Favored : 81.05 % 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 are not related in a simple way. whole: -0.80 (0.18), residues: 2140 helix: 0.76 (0.17), residues: 980 sheet: -1.13 (0.27), residues: 332 loop : -1.83 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 93 TYR 0.021 0.001 TYR E 51 PHE 0.021 0.001 PHE G 75 TRP 0.003 0.000 TRP C 52 HIS 0.004 0.001 HIS G 286 Details of bonding type rmsd covalent geometry : bond 0.00198 (17008) covalent geometry : angle 0.41121 (23008) hydrogen bonds : bond 0.02542 ( 692) hydrogen bonds : angle 4.27225 ( 2040) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 241 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 LEU cc_start: 0.8529 (mt) cc_final: 0.8060 (pp) REVERT: C 281 LEU cc_start: 0.8552 (mt) cc_final: 0.7984 (pp) REVERT: E 281 LEU cc_start: 0.8532 (mt) cc_final: 0.8038 (pp) REVERT: E 326 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7436 (mm-30) REVERT: G 103 GLN cc_start: 0.7819 (tp-100) cc_final: 0.7541 (tp-100) REVERT: G 281 LEU cc_start: 0.8516 (mt) cc_final: 0.8067 (pp) REVERT: G 326 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7480 (mm-30) REVERT: B 132 ARG cc_start: 0.7895 (mtm-85) cc_final: 0.7589 (mtm-85) REVERT: F 132 ARG cc_start: 0.7967 (mtm-85) cc_final: 0.7661 (mtm-85) outliers start: 44 outliers final: 33 residues processed: 273 average time/residue: 0.1380 time to fit residues: 55.3624 Evaluate side-chains 260 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 227 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 33 TYR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain H residue 189 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 116 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 25 optimal weight: 0.0070 chunk 1 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.129387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.103114 restraints weight = 22072.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.104881 restraints weight = 16311.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.106231 restraints weight = 13057.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.107138 restraints weight = 11043.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.107601 restraints weight = 9778.353| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17008 Z= 0.097 Angle : 0.428 9.455 23008 Z= 0.223 Chirality : 0.045 0.146 2688 Planarity : 0.003 0.022 2988 Dihedral : 3.244 12.252 2380 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.07 % Allowed : 17.16 % Favored : 80.77 % 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 are not related in a simple way. whole: -0.63 (0.18), residues: 2140 helix: 0.90 (0.17), residues: 980 sheet: -1.03 (0.27), residues: 332 loop : -1.73 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 93 TYR 0.021 0.001 TYR C 51 PHE 0.022 0.001 PHE G 75 TRP 0.002 0.000 TRP C 52 HIS 0.003 0.001 HIS A 286 Details of bonding type rmsd covalent geometry : bond 0.00227 (17008) covalent geometry : angle 0.42764 (23008) hydrogen bonds : bond 0.02645 ( 692) hydrogen bonds : angle 4.22600 ( 2040) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 238 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 LEU cc_start: 0.8453 (mt) cc_final: 0.8022 (pp) REVERT: C 281 LEU cc_start: 0.8497 (mt) cc_final: 0.7969 (pp) REVERT: E 281 LEU cc_start: 0.8485 (mt) cc_final: 0.8059 (pp) REVERT: G 281 LEU cc_start: 0.8468 (mt) cc_final: 0.8028 (pp) REVERT: B 132 ARG cc_start: 0.7819 (mtm-85) cc_final: 0.7586 (mtm-85) REVERT: F 132 ARG cc_start: 0.7835 (mtm-85) cc_final: 0.7588 (mtm-85) REVERT: H 308 ARG cc_start: 0.7604 (mmp80) cc_final: 0.7254 (mmp80) outliers start: 38 outliers final: 32 residues processed: 263 average time/residue: 0.1356 time to fit residues: 52.7994 Evaluate side-chains 260 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 228 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 87 PHE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain H residue 189 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 209 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 12 optimal weight: 0.0980 chunk 151 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.127453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.103397 restraints weight = 22200.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.103132 restraints weight = 17343.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.103393 restraints weight = 14951.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.103684 restraints weight = 14600.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.104042 restraints weight = 13253.002| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17008 Z= 0.134 Angle : 0.458 10.742 23008 Z= 0.238 Chirality : 0.046 0.147 2688 Planarity : 0.003 0.023 2988 Dihedral : 3.385 14.812 2380 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.85 % Allowed : 17.70 % Favored : 80.45 % 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 are not related in a simple way. whole: -0.62 (0.18), residues: 2140 helix: 0.89 (0.17), residues: 980 sheet: -1.03 (0.27), residues: 332 loop : -1.71 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 93 TYR 0.022 0.001 TYR C 51 PHE 0.023 0.001 PHE G 75 TRP 0.004 0.001 TRP E 123 HIS 0.004 0.001 HIS A 286 Details of bonding type rmsd covalent geometry : bond 0.00326 (17008) covalent geometry : angle 0.45818 (23008) hydrogen bonds : bond 0.02950 ( 692) hydrogen bonds : angle 4.37253 ( 2040) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 232 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 281 LEU cc_start: 0.8482 (mt) cc_final: 0.8054 (pp) REVERT: C 281 LEU cc_start: 0.8521 (mt) cc_final: 0.8010 (pp) REVERT: E 281 LEU cc_start: 0.8525 (mt) cc_final: 0.8093 (pp) REVERT: G 281 LEU cc_start: 0.8478 (mt) cc_final: 0.8048 (pp) outliers start: 34 outliers final: 31 residues processed: 254 average time/residue: 0.1403 time to fit residues: 52.1999 Evaluate side-chains 258 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 227 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 33 TYR Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain H residue 189 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 120 optimal weight: 4.9990 chunk 141 optimal weight: 0.0770 chunk 83 optimal weight: 0.7980 chunk 197 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 72 optimal weight: 0.3980 chunk 76 optimal weight: 0.8980 chunk 111 optimal weight: 0.3980 chunk 193 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.129840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.103692 restraints weight = 21782.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.105513 restraints weight = 16102.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.106693 restraints weight = 12825.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.107681 restraints weight = 10915.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.108212 restraints weight = 9649.001| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17008 Z= 0.087 Angle : 0.442 10.953 23008 Z= 0.228 Chirality : 0.045 0.131 2688 Planarity : 0.003 0.022 2988 Dihedral : 3.257 13.982 2380 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.53 % Allowed : 18.19 % Favored : 80.28 % 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 are not related in a simple way. whole: -0.34 (0.18), residues: 2140 helix: 1.15 (0.17), residues: 980 sheet: -0.83 (0.27), residues: 332 loop : -1.64 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 93 TYR 0.023 0.001 TYR G 51 PHE 0.023 0.001 PHE G 75 TRP 0.002 0.000 TRP A 46 HIS 0.003 0.000 HIS A 286 Details of bonding type rmsd covalent geometry : bond 0.00198 (17008) covalent geometry : angle 0.44239 (23008) hydrogen bonds : bond 0.02505 ( 692) hydrogen bonds : angle 4.23707 ( 2040) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 230 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 281 LEU cc_start: 0.8476 (mt) cc_final: 0.8013 (pp) REVERT: C 281 LEU cc_start: 0.8461 (mt) cc_final: 0.7967 (pp) REVERT: E 281 LEU cc_start: 0.8520 (mt) cc_final: 0.8078 (pp) REVERT: G 281 LEU cc_start: 0.8485 (mt) cc_final: 0.8056 (pp) outliers start: 28 outliers final: 26 residues processed: 250 average time/residue: 0.1355 time to fit residues: 49.6936 Evaluate side-chains 253 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 227 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 87 PHE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain F residue 189 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain H residue 189 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 189 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 134 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.125418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.099000 restraints weight = 22139.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.100715 restraints weight = 16595.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.101827 restraints weight = 13424.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.102685 restraints weight = 11525.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.103346 restraints weight = 10284.416| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17008 Z= 0.198 Angle : 0.516 10.307 23008 Z= 0.266 Chirality : 0.048 0.146 2688 Planarity : 0.003 0.023 2988 Dihedral : 3.613 15.528 2380 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 1.63 % Allowed : 18.63 % Favored : 79.74 % 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 are not related in a simple way. whole: -0.66 (0.18), residues: 2140 helix: 0.81 (0.17), residues: 980 sheet: -0.98 (0.27), residues: 332 loop : -1.71 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 308 TYR 0.023 0.002 TYR C 51 PHE 0.023 0.001 PHE A 75 TRP 0.007 0.001 TRP C 123 HIS 0.005 0.001 HIS A 286 Details of bonding type rmsd covalent geometry : bond 0.00487 (17008) covalent geometry : angle 0.51585 (23008) hydrogen bonds : bond 0.03454 ( 692) hydrogen bonds : angle 4.59799 ( 2040) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2637.87 seconds wall clock time: 46 minutes 15.70 seconds (2775.70 seconds total)