Starting phenix.real_space_refine on Sat Jun 14 23:42:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u6d_20663/06_2025/6u6d_20663.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u6d_20663/06_2025/6u6d_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6u6d_20663/06_2025/6u6d_20663.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u6d_20663/06_2025/6u6d_20663.map" model { file = "/net/cci-nas-00/data/ceres_data/6u6d_20663/06_2025/6u6d_20663.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u6d_20663/06_2025/6u6d_20663.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.87, per 1000 atoms: 0.59 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: 4.57 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.37 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: 5.11 Time building geometry restraints manager: 5.37 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: 0.11 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'A' selection = chain 'C' } 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: 1.020 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: 0.030 Extract box with map and model: 1.110 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 40.410 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.250 ------------------------------------------------------------------------------- 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 : 6.59 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.003 0.001 TRP G 46 HIS 0.002 0.000 HIS A 286 PHE 0.004 0.001 PHE G 75 TYR 0.010 0.001 TYR G 33 ARG 0.003 0.000 ARG G 308 Details of bonding type rmsd hydrogen bonds : bond 0.17568 ( 692) hydrogen bonds : angle 7.03016 ( 2040) covalent geometry : bond 0.00240 (17008) covalent geometry : angle 0.50888 (23008) *********************** 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 : 2.237 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: 0.7347 (tp-100) REVERT: A 146 GLU cc_start: 0.8125 (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: 0.7992 (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: 0.7985 (pp) REVERT: E 96 GLU cc_start: 0.7766 (tt0) cc_final: 0.7561 (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: 0.8014 (pp) REVERT: G 146 GLU cc_start: 0.8115 (tp30) cc_final: 0.7798 (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: 0.7827 (mtt) cc_final: 0.7393 (ttm) REVERT: F 250 MET cc_start: 0.7959 (mtt) cc_final: 0.7552 (ttm) outliers start: 0 outliers final: 0 residues processed: 344 average time/residue: 0.3655 time to fit residues: 174.3193 Evaluate side-chains 250 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.0770 chunk 160 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 166 optimal weight: 0.8980 chunk 64 optimal weight: 10.0000 chunk 101 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 192 optimal weight: 0.8980 overall best weight: 0.7538 ------------------------------------------------------------------------------- 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 C 158 ASN 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.126001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.100636 restraints weight = 22070.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.102385 restraints weight = 16421.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.103593 restraints weight = 13146.854| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1481 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= 0.113 Angle : 0.464 6.594 23008 Z= 0.246 Chirality : 0.046 0.136 2688 Planarity : 0.003 0.041 2988 Dihedral : 3.674 14.571 2380 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.36 % Allowed : 11.38 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.16), residues: 2140 helix: -0.89 (0.16), residues: 972 sheet: -2.40 (0.24), residues: 332 loop : -2.70 (0.16), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 123 HIS 0.002 0.001 HIS D 161 PHE 0.008 0.001 PHE B 251 TYR 0.016 0.001 TYR E 51 ARG 0.006 0.000 ARG A 298 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 692) hydrogen bonds : angle 5.10186 ( 2040) covalent geometry : bond 0.00262 (17008) covalent geometry : angle 0.46446 (23008) *********************** 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 284 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 259 time to evaluate : 1.982 Fit side-chains revert: symmetry clash REVERT: A 281 LEU cc_start: 0.8469 (mt) cc_final: 0.8031 (pp) REVERT: C 281 LEU cc_start: 0.8496 (mt) cc_final: 0.7973 (pp) REVERT: E 281 LEU cc_start: 0.8475 (mt) cc_final: 0.8050 (pp) REVERT: G 281 LEU cc_start: 0.8475 (mt) cc_final: 0.8047 (pp) REVERT: B 151 LYS cc_start: 0.8846 (mtmt) cc_final: 0.8530 (mttt) REVERT: B 250 MET cc_start: 0.8049 (mtt) cc_final: 0.7838 (ttm) REVERT: F 151 LYS cc_start: 0.8814 (mtmt) cc_final: 0.8502 (mttt) outliers start: 25 outliers final: 15 residues processed: 274 average time/residue: 0.3206 time to fit residues: 129.8427 Evaluate side-chains 243 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 228 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE 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 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 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 95 LEU 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 135 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 35 optimal weight: 0.0270 chunk 29 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 78 optimal weight: 0.0970 chunk 91 optimal weight: 6.9990 chunk 49 optimal weight: 0.0770 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN C 219 GLN E 219 GLN G 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.127789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.103567 restraints weight = 21958.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.104605 restraints weight = 18192.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.105546 restraints weight = 15325.028| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 17008 Z= 0.095 Angle : 0.427 6.519 23008 Z= 0.226 Chirality : 0.045 0.155 2688 Planarity : 0.003 0.032 2988 Dihedral : 3.451 12.249 2380 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.53 % Allowed : 13.51 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.17), residues: 2140 helix: -0.32 (0.16), residues: 1000 sheet: -1.86 (0.25), residues: 332 loop : -2.50 (0.17), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP H 123 HIS 0.004 0.001 HIS G 39 PHE 0.006 0.000 PHE A 75 TYR 0.018 0.002 TYR A 65 ARG 0.004 0.000 ARG D 308 Details of bonding type rmsd hydrogen bonds : bond 0.02934 ( 692) hydrogen bonds : angle 4.69328 ( 2040) covalent geometry : bond 0.00217 (17008) covalent geometry : angle 0.42696 (23008) *********************** 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 268 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 240 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 LEU cc_start: 0.8491 (mt) cc_final: 0.7911 (pp) REVERT: C 281 LEU cc_start: 0.8518 (mt) cc_final: 0.7979 (pp) REVERT: C 326 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7360 (mm-30) REVERT: E 281 LEU cc_start: 0.8503 (mt) cc_final: 0.7925 (pp) REVERT: E 326 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7508 (mm-30) REVERT: G 281 LEU cc_start: 0.8496 (mt) cc_final: 0.8000 (pp) REVERT: G 326 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7475 (mm-30) outliers start: 28 outliers final: 22 residues processed: 252 average time/residue: 0.3312 time to fit residues: 122.3395 Evaluate side-chains 240 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 218 time to evaluate : 2.053 ------------------------------------------------------------------------------- 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 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 E residue 264 MET 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 121 optimal weight: 6.9990 chunk 196 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 28 optimal weight: 0.0070 chunk 159 optimal weight: 1.9990 chunk 189 optimal weight: 0.7980 chunk 16 optimal weight: 0.0070 chunk 82 optimal weight: 0.9990 chunk 179 optimal weight: 0.6980 chunk 140 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 overall best weight: 0.4416 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.148449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.126637 restraints weight = 20801.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.127212 restraints weight = 18956.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.127853 restraints weight = 14673.328| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 17008 Z= 0.081 Angle : 0.406 6.065 23008 Z= 0.215 Chirality : 0.045 0.138 2688 Planarity : 0.003 0.027 2988 Dihedral : 3.282 11.713 2380 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.74 % Allowed : 14.60 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.17), residues: 2140 helix: 0.25 (0.17), residues: 976 sheet: -1.36 (0.27), residues: 332 loop : -2.26 (0.17), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP G 52 HIS 0.003 0.001 HIS G 39 PHE 0.004 0.000 PHE E 75 TYR 0.018 0.001 TYR G 51 ARG 0.005 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.02575 ( 692) hydrogen bonds : angle 4.44609 ( 2040) covalent geometry : bond 0.00181 (17008) covalent geometry : angle 0.40583 (23008) *********************** 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 270 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 238 time to evaluate : 2.043 Fit side-chains REVERT: A 103 GLN cc_start: 0.7907 (tp-100) cc_final: 0.7515 (tp-100) REVERT: A 281 LEU cc_start: 0.8412 (mt) cc_final: 0.7949 (pp) REVERT: A 326 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7317 (mm-30) REVERT: C 281 LEU cc_start: 0.8456 (mt) cc_final: 0.7946 (pp) REVERT: C 326 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7310 (mm-30) REVERT: E 281 LEU cc_start: 0.8440 (mt) cc_final: 0.7995 (pp) REVERT: G 281 LEU cc_start: 0.8351 (mt) cc_final: 0.7959 (pp) REVERT: G 326 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7404 (mm-30) REVERT: F 132 ARG cc_start: 0.7739 (mtm-85) cc_final: 0.7513 (mtm-85) REVERT: H 132 ARG cc_start: 0.7733 (mtm-85) cc_final: 0.7492 (mtm-85) outliers start: 32 outliers final: 26 residues processed: 256 average time/residue: 0.3232 time to fit residues: 119.9649 Evaluate side-chains 246 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 220 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL 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 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 87 PHE 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 87 PHE 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 58 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 198 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 80 optimal weight: 0.0770 chunk 82 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- 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 = 0.3422 r_free = 0.3422 target = 0.127924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.103860 restraints weight = 22269.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.103831 restraints weight = 17048.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.104048 restraints weight = 14675.189| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17008 Z= 0.118 Angle : 0.433 6.405 23008 Z= 0.228 Chirality : 0.046 0.147 2688 Planarity : 0.003 0.030 2988 Dihedral : 3.357 12.645 2380 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.07 % Allowed : 15.36 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.17), residues: 2140 helix: 0.43 (0.17), residues: 976 sheet: -1.27 (0.27), residues: 332 loop : -2.10 (0.18), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 52 HIS 0.004 0.001 HIS A 286 PHE 0.020 0.001 PHE E 38 TYR 0.019 0.001 TYR G 51 ARG 0.007 0.000 ARG D 308 Details of bonding type rmsd hydrogen bonds : bond 0.02897 ( 692) hydrogen bonds : angle 4.46808 ( 2040) covalent geometry : bond 0.00283 (17008) covalent geometry : angle 0.43309 (23008) *********************** 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 268 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 230 time to evaluate : 1.957 Fit side-chains REVERT: A 103 GLN cc_start: 0.7872 (tp-100) cc_final: 0.7583 (tp-100) REVERT: A 281 LEU cc_start: 0.8430 (mt) cc_final: 0.7986 (pp) REVERT: C 281 LEU cc_start: 0.8524 (mt) cc_final: 0.7980 (pp) REVERT: E 281 LEU cc_start: 0.8532 (mt) cc_final: 0.7993 (pp) REVERT: G 281 LEU cc_start: 0.8493 (mt) cc_final: 0.8066 (pp) REVERT: B 132 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7479 (mtp-110) REVERT: F 132 ARG cc_start: 0.7926 (mtm-85) cc_final: 0.7689 (mtm-85) outliers start: 38 outliers final: 27 residues processed: 253 average time/residue: 0.3267 time to fit residues: 119.2324 Evaluate side-chains 250 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 30 VAL 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 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 95 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain B residue 132 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 49 optimal weight: 0.0770 chunk 30 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 25 optimal weight: 0.0270 chunk 170 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.0202 ------------------------------------------------------------------------------- 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 = 0.3416 r_free = 0.3416 target = 0.127567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.103307 restraints weight = 22043.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.103243 restraints weight = 16773.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.103497 restraints weight = 14409.874| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2316 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= 0.119 Angle : 0.429 7.306 23008 Z= 0.225 Chirality : 0.046 0.138 2688 Planarity : 0.003 0.041 2988 Dihedral : 3.342 13.650 2380 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.23 % Allowed : 15.52 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.17), residues: 2140 helix: 0.51 (0.17), residues: 980 sheet: -1.12 (0.26), residues: 348 loop : -1.96 (0.19), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 52 HIS 0.005 0.001 HIS E 286 PHE 0.013 0.001 PHE E 38 TYR 0.021 0.001 TYR C 51 ARG 0.004 0.000 ARG C 93 Details of bonding type rmsd hydrogen bonds : bond 0.02840 ( 692) hydrogen bonds : angle 4.45543 ( 2040) covalent geometry : bond 0.00285 (17008) covalent geometry : angle 0.42920 (23008) *********************** 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 269 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 228 time to evaluate : 1.854 Fit side-chains revert: symmetry clash REVERT: A 103 GLN cc_start: 0.7844 (tp-100) cc_final: 0.7552 (tp-100) REVERT: A 151 LYS cc_start: 0.9032 (mttt) cc_final: 0.8818 (mttt) REVERT: A 281 LEU cc_start: 0.8499 (mt) cc_final: 0.8031 (pp) REVERT: C 281 LEU cc_start: 0.8503 (mt) cc_final: 0.7967 (pp) REVERT: C 326 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7371 (mm-30) REVERT: E 281 LEU cc_start: 0.8476 (mt) cc_final: 0.8056 (pp) REVERT: G 281 LEU cc_start: 0.8488 (mt) cc_final: 0.8060 (pp) REVERT: G 326 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7458 (mm-30) REVERT: B 132 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7577 (mtp-110) REVERT: F 132 ARG cc_start: 0.7933 (mtm-85) cc_final: 0.7655 (mtm-85) outliers start: 41 outliers final: 31 residues processed: 252 average time/residue: 0.3135 time to fit residues: 115.6371 Evaluate side-chains 255 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 223 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 30 VAL 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 30 VAL 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 132 ARG Chi-restraints excluded: chain F residue 281 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 26 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 72 optimal weight: 0.0370 chunk 203 optimal weight: 3.9990 chunk 147 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.8660 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.128110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.101954 restraints weight = 21874.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.103710 restraints weight = 16314.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.104960 restraints weight = 13131.847| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17008 Z= 0.108 Angle : 0.426 6.725 23008 Z= 0.223 Chirality : 0.045 0.146 2688 Planarity : 0.003 0.022 2988 Dihedral : 3.302 13.003 2380 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.23 % Allowed : 16.29 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.18), residues: 2140 helix: 0.66 (0.17), residues: 980 sheet: -1.16 (0.27), residues: 332 loop : -1.87 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 52 HIS 0.004 0.001 HIS E 286 PHE 0.020 0.001 PHE A 75 TYR 0.021 0.001 TYR G 51 ARG 0.004 0.000 ARG E 93 Details of bonding type rmsd hydrogen bonds : bond 0.02763 ( 692) hydrogen bonds : angle 4.36929 ( 2040) covalent geometry : bond 0.00258 (17008) covalent geometry : angle 0.42614 (23008) *********************** 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 275 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 234 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 LYS cc_start: 0.9006 (mttt) cc_final: 0.8797 (mttt) REVERT: A 281 LEU cc_start: 0.8496 (mt) cc_final: 0.8023 (pp) REVERT: C 151 LYS cc_start: 0.9012 (mttt) cc_final: 0.8797 (mttt) REVERT: C 281 LEU cc_start: 0.8496 (mt) cc_final: 0.8002 (pp) REVERT: E 281 LEU cc_start: 0.8518 (mt) cc_final: 0.8044 (pp) REVERT: G 151 LYS cc_start: 0.9008 (mttt) cc_final: 0.8797 (mttt) REVERT: G 281 LEU cc_start: 0.8486 (mt) cc_final: 0.8045 (pp) REVERT: B 132 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7571 (mtp-110) REVERT: F 308 ARG cc_start: 0.7875 (mmp80) cc_final: 0.7396 (mtt-85) outliers start: 41 outliers final: 32 residues processed: 261 average time/residue: 0.3184 time to fit residues: 122.3098 Evaluate side-chains 254 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 221 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 30 VAL 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 30 VAL 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 132 ARG Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain F residue 281 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 67 optimal weight: 4.9990 chunk 143 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 chunk 178 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3423 r_free = 0.3423 target = 0.127938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.103564 restraints weight = 21985.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.103924 restraints weight = 15711.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.104653 restraints weight = 12633.416| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17008 Z= 0.113 Angle : 0.435 6.583 23008 Z= 0.227 Chirality : 0.046 0.146 2688 Planarity : 0.003 0.022 2988 Dihedral : 3.309 14.280 2380 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.34 % Allowed : 16.67 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.18), residues: 2140 helix: 0.79 (0.17), residues: 980 sheet: -1.09 (0.27), residues: 332 loop : -1.81 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 52 HIS 0.004 0.001 HIS E 286 PHE 0.021 0.001 PHE A 75 TYR 0.022 0.001 TYR E 51 ARG 0.005 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.02782 ( 692) hydrogen bonds : angle 4.36302 ( 2040) covalent geometry : bond 0.00271 (17008) covalent geometry : angle 0.43458 (23008) *********************** 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 270 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 227 time to evaluate : 2.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 LYS cc_start: 0.9057 (mttt) cc_final: 0.8844 (mttt) REVERT: A 281 LEU cc_start: 0.8486 (mt) cc_final: 0.8022 (pp) REVERT: C 151 LYS cc_start: 0.9049 (mttt) cc_final: 0.8832 (mttt) REVERT: C 281 LEU cc_start: 0.8462 (mt) cc_final: 0.7994 (pp) REVERT: E 281 LEU cc_start: 0.8500 (mt) cc_final: 0.8043 (pp) REVERT: G 103 GLN cc_start: 0.7922 (tp-100) cc_final: 0.7701 (tp-100) REVERT: G 151 LYS cc_start: 0.9052 (mttt) cc_final: 0.8836 (mttt) REVERT: G 281 LEU cc_start: 0.8488 (mt) cc_final: 0.8091 (pp) REVERT: B 132 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7446 (mtp-110) REVERT: F 308 ARG cc_start: 0.7854 (mmp80) cc_final: 0.7326 (mtt-85) outliers start: 43 outliers final: 35 residues processed: 254 average time/residue: 0.3984 time to fit residues: 150.4712 Evaluate side-chains 257 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 221 time to evaluate : 2.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 30 VAL 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 30 VAL 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 87 PHE Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 150 LYS Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain B residue 132 ARG 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 102 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 140 optimal weight: 0.0970 chunk 175 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.128055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.103765 restraints weight = 22004.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.103687 restraints weight = 16768.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.103986 restraints weight = 14451.649| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17008 Z= 0.114 Angle : 0.445 10.564 23008 Z= 0.231 Chirality : 0.046 0.143 2688 Planarity : 0.003 0.022 2988 Dihedral : 3.309 14.185 2380 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.96 % Allowed : 17.21 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.18), residues: 2140 helix: 0.91 (0.17), residues: 980 sheet: -1.00 (0.27), residues: 332 loop : -1.73 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 52 HIS 0.004 0.001 HIS E 286 PHE 0.022 0.001 PHE A 75 TYR 0.022 0.001 TYR G 51 ARG 0.005 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.02771 ( 692) hydrogen bonds : angle 4.36383 ( 2040) covalent geometry : bond 0.00275 (17008) covalent geometry : angle 0.44455 (23008) *********************** 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 264 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 228 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 LEU cc_start: 0.8515 (mt) cc_final: 0.8027 (pp) REVERT: C 151 LYS cc_start: 0.9009 (mttt) cc_final: 0.8808 (mttt) REVERT: C 281 LEU cc_start: 0.8485 (mt) cc_final: 0.8012 (pp) REVERT: E 103 GLN cc_start: 0.7736 (tp-100) cc_final: 0.7490 (tp-100) REVERT: E 281 LEU cc_start: 0.8542 (mt) cc_final: 0.8073 (pp) REVERT: G 281 LEU cc_start: 0.8549 (mt) cc_final: 0.8106 (pp) REVERT: B 132 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7577 (mtp-110) REVERT: F 308 ARG cc_start: 0.7990 (mmp80) cc_final: 0.7465 (mtt-85) outliers start: 36 outliers final: 32 residues processed: 251 average time/residue: 0.3793 time to fit residues: 139.1946 Evaluate side-chains 257 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 224 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU 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 187 SER Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 30 VAL 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 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 150 LYS Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain B residue 132 ARG 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 72 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 157 optimal weight: 0.0870 chunk 57 optimal weight: 4.9990 chunk 97 optimal weight: 0.0980 chunk 171 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 4 optimal weight: 0.0670 chunk 178 optimal weight: 0.5980 chunk 199 optimal weight: 0.8980 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.131097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.104972 restraints weight = 21744.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.106793 restraints weight = 16042.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.107988 restraints weight = 12779.484| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17008 Z= 0.079 Angle : 0.426 10.673 23008 Z= 0.220 Chirality : 0.045 0.135 2688 Planarity : 0.003 0.021 2988 Dihedral : 3.140 12.617 2380 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.42 % Allowed : 18.08 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.18), residues: 2140 helix: 1.24 (0.17), residues: 976 sheet: -0.81 (0.27), residues: 332 loop : -1.63 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 52 HIS 0.003 0.001 HIS G 286 PHE 0.023 0.001 PHE A 75 TYR 0.022 0.001 TYR C 51 ARG 0.006 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.02391 ( 692) hydrogen bonds : angle 4.12495 ( 2040) covalent geometry : bond 0.00174 (17008) covalent geometry : angle 0.42556 (23008) ********************** 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 271 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 245 time to evaluate : 2.037 Fit side-chains REVERT: A 281 LEU cc_start: 0.8494 (mt) cc_final: 0.7996 (pp) REVERT: C 151 LYS cc_start: 0.9013 (mttt) cc_final: 0.8805 (mttt) REVERT: C 281 LEU cc_start: 0.8527 (mt) cc_final: 0.8024 (pp) REVERT: E 281 LEU cc_start: 0.8509 (mt) cc_final: 0.8043 (pp) REVERT: G 281 LEU cc_start: 0.8522 (mt) cc_final: 0.8071 (pp) REVERT: B 132 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7475 (mtp-110) REVERT: F 308 ARG cc_start: 0.7919 (mmp80) cc_final: 0.7483 (mtt-85) outliers start: 26 outliers final: 21 residues processed: 262 average time/residue: 0.3118 time to fit residues: 120.2956 Evaluate side-chains 245 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 87 PHE Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain D 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 86 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 134 optimal weight: 0.0060 chunk 190 optimal weight: 1.9990 chunk 182 optimal weight: 0.9990 chunk 173 optimal weight: 0.0010 chunk 135 optimal weight: 0.3980 chunk 13 optimal weight: 0.0980 chunk 89 optimal weight: 5.9990 overall best weight: 0.2202 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.151220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3469 r_free = 0.3469 target = 0.132274 restraints weight = 20845.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.132817 restraints weight = 17032.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.132969 restraints weight = 14526.840| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17008 Z= 0.079 Angle : 0.441 10.478 23008 Z= 0.227 Chirality : 0.045 0.164 2688 Planarity : 0.003 0.024 2988 Dihedral : 3.099 14.071 2380 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.31 % Allowed : 18.52 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.18), residues: 2140 helix: 1.40 (0.17), residues: 976 sheet: -0.62 (0.27), residues: 332 loop : -1.52 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 52 HIS 0.003 0.001 HIS A 286 PHE 0.021 0.001 PHE A 75 TYR 0.022 0.001 TYR G 51 ARG 0.010 0.000 ARG D 308 Details of bonding type rmsd hydrogen bonds : bond 0.02370 ( 692) hydrogen bonds : angle 4.01996 ( 2040) covalent geometry : bond 0.00172 (17008) covalent geometry : angle 0.44091 (23008) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5855.09 seconds wall clock time: 103 minutes 58.90 seconds (6238.90 seconds total)