Starting phenix.real_space_refine on Sat Jul 4 11:39:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7q13_13753/07_2026/7q13_13753.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q13_13753/07_2026/7q13_13753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7q13_13753/07_2026/7q13_13753.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7q13_13753/07_2026/7q13_13753.cif" model { file = "/net/cci-nas-00/data/ceres_data/7q13_13753/07_2026/7q13_13753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q13_13753/07_2026/7q13_13753.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q13_13753/07_2026/7q13_13753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q13_13753/07_2026/7q13_13753.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 P 12 5.49 5 S 108 5.16 5 C 12996 2.51 5 N 3500 2.21 5 O 3752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20368 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4767 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 590, 4759 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} Conformer: "B" Number of residues, atoms: 590, 4759 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} bond proxies already assigned to first conformer: 4876 Chain: "E" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 272 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "F" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 272 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "G" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 272 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "H" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 272 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "B" Number of atoms: 4767 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 590, 4759 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} Conformer: "B" Number of residues, atoms: 590, 4759 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} bond proxies already assigned to first conformer: 4876 Chain: "C" Number of atoms: 4767 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 590, 4759 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} Conformer: "B" Number of residues, atoms: 590, 4759 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} bond proxies already assigned to first conformer: 4876 Chain: "D" Number of atoms: 4767 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 590, 4759 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} Conformer: "B" Number of residues, atoms: 590, 4759 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 23, 'TRANS': 566} bond proxies already assigned to first conformer: 4876 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'G6P': 1, 'GLC': 1, 'UDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'G6P': 1, 'GLC': 1, 'UDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'G6P': 1, 'GLC': 1, 'UDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 53 Unusual residues: {'G6P': 1, 'GLC': 1, 'UDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" C1 GLC A 803 " occ=0.50 ... (10 atoms not shown) pdb=" O6 GLC A 803 " occ=0.50 residue: pdb=" C1 GLC B 803 " occ=0.50 ... (10 atoms not shown) pdb=" O6 GLC B 803 " occ=0.50 residue: pdb=" C1 GLC C 803 " occ=0.50 ... (10 atoms not shown) pdb=" O6 GLC C 803 " occ=0.50 residue: pdb=" C1 GLC D 803 " occ=0.50 ... (10 atoms not shown) pdb=" O6 GLC D 803 " occ=0.50 Time building chain proxies: 6.19, per 1000 atoms: 0.30 Number of scatterers: 20368 At special positions: 0 Unit cell: (113.42, 137.8, 121.9, 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) S 108 16.00 P 12 15.00 O 3752 8.00 N 3500 7.00 C 12996 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 1.2 seconds 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4664 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 12 sheets defined 51.3% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 43 through 57 removed outlier: 4.589A pdb=" N LYS A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 137 removed outlier: 3.531A pdb=" N TRP A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 169 removed outlier: 3.778A pdb=" N ASN A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 185 through 195 removed outlier: 4.187A pdb=" N CYS A 189 " --> pdb=" O GLY A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 239 through 252 Processing helix chain 'A' and resid 259 through 270 Processing helix chain 'A' and resid 291 through 312 Processing helix chain 'A' and resid 339 through 356 Processing helix chain 'A' and resid 376 through 411 removed outlier: 3.637A pdb=" N LEU A 380 " --> pdb=" O ASN A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 435 removed outlier: 3.752A pdb=" N PHE A 425 " --> pdb=" O ASP A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 463 Processing helix chain 'A' and resid 492 through 500 Processing helix chain 'A' and resid 514 through 522 Processing helix chain 'A' and resid 532 through 540 removed outlier: 3.716A pdb=" N GLU A 540 " --> pdb=" O CYS A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 577 removed outlier: 3.684A pdb=" N GLN A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 591 Processing helix chain 'A' and resid 592 through 596 Processing helix chain 'A' and resid 597 through 602 Processing helix chain 'A' and resid 602 through 617 Processing helix chain 'E' and resid 319 through 328 Processing helix chain 'E' and resid 337 through 346 removed outlier: 4.234A pdb=" N ILE E 341 " --> pdb=" O SER E 337 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP E 346 " --> pdb=" O LYS E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 349 No H-bonds generated for 'chain 'E' and resid 347 through 349' Processing helix chain 'F' and resid 319 through 328 Processing helix chain 'F' and resid 337 through 346 removed outlier: 4.234A pdb=" N ILE F 341 " --> pdb=" O SER F 337 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 349 No H-bonds generated for 'chain 'F' and resid 347 through 349' Processing helix chain 'G' and resid 319 through 328 Processing helix chain 'G' and resid 337 through 346 removed outlier: 4.234A pdb=" N ILE G 341 " --> pdb=" O SER G 337 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP G 346 " --> pdb=" O LYS G 342 " (cutoff:3.500A) Processing helix chain 'G' and resid 347 through 349 No H-bonds generated for 'chain 'G' and resid 347 through 349' Processing helix chain 'H' and resid 319 through 328 Processing helix chain 'H' and resid 337 through 346 removed outlier: 4.235A pdb=" N ILE H 341 " --> pdb=" O SER H 337 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP H 346 " --> pdb=" O LYS H 342 " (cutoff:3.500A) Processing helix chain 'H' and resid 347 through 349 No H-bonds generated for 'chain 'H' and resid 347 through 349' Processing helix chain 'B' and resid 43 through 57 removed outlier: 4.589A pdb=" N LYS B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 137 removed outlier: 3.532A pdb=" N TRP B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 169 removed outlier: 3.778A pdb=" N ASN B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 185 through 195 removed outlier: 4.187A pdb=" N CYS B 189 " --> pdb=" O GLY B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 215 Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'B' and resid 239 through 252 Processing helix chain 'B' and resid 259 through 270 Processing helix chain 'B' and resid 291 through 312 Processing helix chain 'B' and resid 339 through 356 Processing helix chain 'B' and resid 376 through 411 removed outlier: 3.637A pdb=" N LEU B 380 " --> pdb=" O ASN B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 435 removed outlier: 3.752A pdb=" N PHE B 425 " --> pdb=" O ASP B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 463 Processing helix chain 'B' and resid 492 through 500 Processing helix chain 'B' and resid 514 through 522 Processing helix chain 'B' and resid 532 through 540 removed outlier: 3.716A pdb=" N GLU B 540 " --> pdb=" O CYS B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 577 removed outlier: 3.684A pdb=" N GLN B 577 " --> pdb=" O SER B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 591 Processing helix chain 'B' and resid 592 through 596 Processing helix chain 'B' and resid 597 through 602 Processing helix chain 'B' and resid 602 through 617 Processing helix chain 'C' and resid 43 through 57 removed outlier: 4.589A pdb=" N LYS C 52 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL C 53 " --> pdb=" O THR C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 137 removed outlier: 3.531A pdb=" N TRP C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 169 removed outlier: 3.778A pdb=" N ASN C 149 " --> pdb=" O ASP C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 184 No H-bonds generated for 'chain 'C' and resid 182 through 184' Processing helix chain 'C' and resid 185 through 195 removed outlier: 4.186A pdb=" N CYS C 189 " --> pdb=" O GLY C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 215 Processing helix chain 'C' and resid 228 through 233 Processing helix chain 'C' and resid 239 through 252 Processing helix chain 'C' and resid 259 through 270 Processing helix chain 'C' and resid 291 through 312 Processing helix chain 'C' and resid 339 through 356 Processing helix chain 'C' and resid 376 through 411 removed outlier: 3.638A pdb=" N LEU C 380 " --> pdb=" O ASN C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 435 removed outlier: 3.752A pdb=" N PHE C 425 " --> pdb=" O ASP C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 463 Processing helix chain 'C' and resid 492 through 500 Processing helix chain 'C' and resid 514 through 522 Processing helix chain 'C' and resid 532 through 540 removed outlier: 3.716A pdb=" N GLU C 540 " --> pdb=" O CYS C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 577 removed outlier: 3.684A pdb=" N GLN C 577 " --> pdb=" O SER C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 591 Processing helix chain 'C' and resid 592 through 596 Processing helix chain 'C' and resid 597 through 602 Processing helix chain 'C' and resid 602 through 617 Processing helix chain 'D' and resid 43 through 57 removed outlier: 4.590A pdb=" N LYS D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL D 53 " --> pdb=" O THR D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 137 removed outlier: 3.531A pdb=" N TRP D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 169 removed outlier: 3.778A pdb=" N ASN D 149 " --> pdb=" O ASP D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 184 No H-bonds generated for 'chain 'D' and resid 182 through 184' Processing helix chain 'D' and resid 185 through 195 removed outlier: 4.187A pdb=" N CYS D 189 " --> pdb=" O GLY D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 215 Processing helix chain 'D' and resid 228 through 233 Processing helix chain 'D' and resid 239 through 252 Processing helix chain 'D' and resid 259 through 270 Processing helix chain 'D' and resid 291 through 312 Processing helix chain 'D' and resid 339 through 356 Processing helix chain 'D' and resid 376 through 411 removed outlier: 3.637A pdb=" N LEU D 380 " --> pdb=" O ASN D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 435 removed outlier: 3.752A pdb=" N PHE D 425 " --> pdb=" O ASP D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 463 Processing helix chain 'D' and resid 492 through 500 Processing helix chain 'D' and resid 514 through 522 Processing helix chain 'D' and resid 532 through 540 removed outlier: 3.716A pdb=" N GLU D 540 " --> pdb=" O CYS D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 577 removed outlier: 3.684A pdb=" N GLN D 577 " --> pdb=" O SER D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 591 Processing helix chain 'D' and resid 592 through 596 Processing helix chain 'D' and resid 597 through 602 Processing helix chain 'D' and resid 602 through 617 Processing sheet with id=AA1, first strand: chain 'A' and resid 101 through 104 removed outlier: 6.189A pdb=" N LEU A 64 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU A 117 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLY A 66 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A 65 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N PHE A 30 " --> pdb=" O HIS A 178 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N HIS A 180 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL A 32 " --> pdb=" O HIS A 180 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA A 177 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N THR A 203 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N PHE A 179 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE A 276 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR A 257 " --> pdb=" O ILE A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 473 through 477 removed outlier: 6.520A pdb=" N VAL A 362 " --> pdb=" O LYS A 474 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE A 476 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ALA A 364 " --> pdb=" O ILE A 476 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU A 324 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N PHE A 365 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE A 326 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N LEU A 502 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR A 325 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N VAL A 504 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N PHE A 327 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLY A 503 " --> pdb=" O ILE A 527 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 372 through 375 removed outlier: 3.983A pdb=" N ASN A 374 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 104 removed outlier: 6.188A pdb=" N LEU B 64 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU B 117 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLY B 66 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL B 65 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N PHE B 30 " --> pdb=" O HIS B 178 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N HIS B 180 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL B 32 " --> pdb=" O HIS B 180 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA B 177 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N THR B 203 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N PHE B 179 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE B 276 " --> pdb=" O PHE B 255 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR B 257 " --> pdb=" O ILE B 276 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 477 removed outlier: 6.520A pdb=" N VAL B 362 " --> pdb=" O LYS B 474 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE B 476 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ALA B 364 " --> pdb=" O ILE B 476 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU B 324 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N PHE B 365 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE B 326 " --> pdb=" O PHE B 365 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N LEU B 502 " --> pdb=" O THR B 323 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR B 325 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL B 504 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N PHE B 327 " --> pdb=" O VAL B 504 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLY B 503 " --> pdb=" O ILE B 527 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 372 through 375 removed outlier: 3.983A pdb=" N ASN B 374 " --> pdb=" O ASN B 447 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 101 through 104 removed outlier: 6.188A pdb=" N LEU C 64 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU C 117 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLY C 66 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL C 65 " --> pdb=" O GLU C 31 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N PHE C 30 " --> pdb=" O HIS C 178 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N HIS C 180 " --> pdb=" O PHE C 30 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL C 32 " --> pdb=" O HIS C 180 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA C 177 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N THR C 203 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N PHE C 179 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE C 276 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR C 257 " --> pdb=" O ILE C 276 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 473 through 477 removed outlier: 6.520A pdb=" N VAL C 362 " --> pdb=" O LYS C 474 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE C 476 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ALA C 364 " --> pdb=" O ILE C 476 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU C 324 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N PHE C 365 " --> pdb=" O LEU C 324 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE C 326 " --> pdb=" O PHE C 365 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N LEU C 502 " --> pdb=" O THR C 323 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR C 325 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL C 504 " --> pdb=" O TYR C 325 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N PHE C 327 " --> pdb=" O VAL C 504 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLY C 503 " --> pdb=" O ILE C 527 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 372 through 375 removed outlier: 3.983A pdb=" N ASN C 374 " --> pdb=" O ASN C 447 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 101 through 104 removed outlier: 6.188A pdb=" N LEU D 64 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU D 117 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLY D 66 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL D 65 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N PHE D 30 " --> pdb=" O HIS D 178 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N HIS D 180 " --> pdb=" O PHE D 30 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL D 32 " --> pdb=" O HIS D 180 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA D 177 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N THR D 203 " --> pdb=" O ALA D 177 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N PHE D 179 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE D 276 " --> pdb=" O PHE D 255 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR D 257 " --> pdb=" O ILE D 276 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 473 through 477 removed outlier: 6.520A pdb=" N VAL D 362 " --> pdb=" O LYS D 474 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE D 476 " --> pdb=" O VAL D 362 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ALA D 364 " --> pdb=" O ILE D 476 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LEU D 324 " --> pdb=" O VAL D 363 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N PHE D 365 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE D 326 " --> pdb=" O PHE D 365 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N LEU D 502 " --> pdb=" O THR D 323 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR D 325 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N VAL D 504 " --> pdb=" O TYR D 325 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N PHE D 327 " --> pdb=" O VAL D 504 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N GLY D 503 " --> pdb=" O ILE D 527 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 372 through 375 removed outlier: 3.983A pdb=" N ASN D 374 " --> pdb=" O ASN D 447 " (cutoff:3.500A) 884 hydrogen bonds defined for protein. 2612 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: 3.50 Time building geometry restraints manager: 2.11 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: 6580 1.34 - 1.46: 5064 1.46 - 1.58: 9072 1.58 - 1.69: 16 1.69 - 1.81: 164 Bond restraints: 20896 Sorted by residual: bond pdb=" N3 UDP C 802 " pdb=" C4 UDP C 802 " ideal model delta sigma weight residual 1.383 1.331 0.052 1.20e-02 6.94e+03 1.86e+01 bond pdb=" N3 UDP A 802 " pdb=" C4 UDP A 802 " ideal model delta sigma weight residual 1.383 1.331 0.052 1.20e-02 6.94e+03 1.85e+01 bond pdb=" N3 UDP D 802 " pdb=" C4 UDP D 802 " ideal model delta sigma weight residual 1.383 1.332 0.051 1.20e-02 6.94e+03 1.82e+01 bond pdb=" N3 UDP B 802 " pdb=" C4 UDP B 802 " ideal model delta sigma weight residual 1.383 1.332 0.051 1.20e-02 6.94e+03 1.78e+01 bond pdb=" N1 UDP C 802 " pdb=" C6 UDP C 802 " ideal model delta sigma weight residual 1.375 1.334 0.041 1.00e-02 1.00e+04 1.65e+01 ... (remaining 20891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 27463 1.84 - 3.68: 664 3.68 - 5.52: 147 5.52 - 7.37: 42 7.37 - 9.21: 12 Bond angle restraints: 28328 Sorted by residual: angle pdb=" O3A UDP C 802 " pdb=" PB UDP C 802 " pdb=" O3B UDP C 802 " ideal model delta sigma weight residual 112.01 102.80 9.21 1.00e+00 1.00e+00 8.48e+01 angle pdb=" O3A UDP B 802 " pdb=" PB UDP B 802 " pdb=" O3B UDP B 802 " ideal model delta sigma weight residual 112.01 102.84 9.17 1.00e+00 1.00e+00 8.41e+01 angle pdb=" O3A UDP A 802 " pdb=" PB UDP A 802 " pdb=" O3B UDP A 802 " ideal model delta sigma weight residual 112.01 102.84 9.17 1.00e+00 1.00e+00 8.40e+01 angle pdb=" O3A UDP D 802 " pdb=" PB UDP D 802 " pdb=" O3B UDP D 802 " ideal model delta sigma weight residual 112.01 102.85 9.16 1.00e+00 1.00e+00 8.39e+01 angle pdb=" C2 UDP D 802 " pdb=" N3 UDP D 802 " pdb=" C4 UDP D 802 " ideal model delta sigma weight residual 126.93 120.14 6.79 1.00e+00 1.00e+00 4.61e+01 ... (remaining 28323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 10904 17.84 - 35.69: 1024 35.69 - 53.53: 224 53.53 - 71.37: 36 71.37 - 89.22: 32 Dihedral angle restraints: 12220 sinusoidal: 4964 harmonic: 7256 Sorted by residual: dihedral pdb=" CG ARG A 236 " pdb=" CD ARG A 236 " pdb=" NE ARG A 236 " pdb=" CZ ARG A 236 " ideal model delta sinusoidal sigma weight residual -90.00 -134.48 44.48 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG B 236 " pdb=" CD ARG B 236 " pdb=" NE ARG B 236 " pdb=" CZ ARG B 236 " ideal model delta sinusoidal sigma weight residual -90.00 -134.46 44.46 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG D 236 " pdb=" CD ARG D 236 " pdb=" NE ARG D 236 " pdb=" CZ ARG D 236 " ideal model delta sinusoidal sigma weight residual -90.00 -134.46 44.46 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 12217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.020: 3020 1.020 - 2.039: 0 2.039 - 3.059: 0 3.059 - 4.078: 0 4.078 - 5.098: 20 Chirality restraints: 3040 Sorted by residual: chirality pdb=" C5 G6P C 801 " pdb=" C4 G6P C 801 " pdb=" C6 G6P C 801 " pdb=" O5 G6P C 801 " both_signs ideal model delta sigma weight residual False -2.51 2.58 -5.10 2.00e-01 2.50e+01 6.50e+02 chirality pdb=" C5 G6P A 801 " pdb=" C4 G6P A 801 " pdb=" C6 G6P A 801 " pdb=" O5 G6P A 801 " both_signs ideal model delta sigma weight residual False -2.51 2.58 -5.09 2.00e-01 2.50e+01 6.49e+02 chirality pdb=" C5 G6P D 801 " pdb=" C4 G6P D 801 " pdb=" C6 G6P D 801 " pdb=" O5 G6P D 801 " both_signs ideal model delta sigma weight residual False -2.51 2.58 -5.09 2.00e-01 2.50e+01 6.48e+02 ... (remaining 3037 not shown) Planarity restraints: 3612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 106 " 0.020 2.00e-02 2.50e+03 1.85e-02 8.53e+00 pdb=" CG TRP A 106 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP A 106 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 106 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 106 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 106 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 106 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 106 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 106 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 106 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 106 " 0.020 2.00e-02 2.50e+03 1.84e-02 8.46e+00 pdb=" CG TRP D 106 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP D 106 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP D 106 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 106 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 106 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 106 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 106 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 106 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP D 106 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 106 " -0.020 2.00e-02 2.50e+03 1.84e-02 8.46e+00 pdb=" CG TRP C 106 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP C 106 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP C 106 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 106 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 106 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 106 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 106 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 106 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP C 106 " -0.001 2.00e-02 2.50e+03 ... (remaining 3609 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2176 2.75 - 3.28: 20326 3.28 - 3.82: 34949 3.82 - 4.36: 42224 4.36 - 4.90: 71031 Nonbonded interactions: 170706 Sorted by model distance: nonbonded pdb=" OE2 GLU B 406 " pdb=" NH2 ARG C 309 " model vdw 2.208 3.120 nonbonded pdb=" OE2 GLU B 292 " pdb=" O3 G6P D 801 " model vdw 2.224 3.040 nonbonded pdb=" OE2 GLU A 292 " pdb=" O3 G6P C 801 " model vdw 2.230 3.040 nonbonded pdb=" OE2 GLU D 292 " pdb=" O3 G6P B 801 " model vdw 2.231 3.040 nonbonded pdb=" OE2 GLU C 292 " pdb=" O3 G6P A 801 " model vdw 2.270 3.040 ... (remaining 170701 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 20.920 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 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 : 0.004 0.076 20896 Z= 0.239 Angle : 0.712 9.208 28328 Z= 0.411 Chirality : 0.389 5.098 3040 Planarity : 0.004 0.055 3612 Dihedral : 15.063 89.218 7556 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.12 % Allowed : 0.75 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.18), residues: 2476 helix: 1.34 (0.15), residues: 1232 sheet: -1.32 (0.29), residues: 300 loop : -1.36 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 343 TYR 0.019 0.001 TYR G 348 PHE 0.013 0.001 PHE B 103 TRP 0.049 0.002 TRP A 106 HIS 0.004 0.001 HIS B 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.24 (20896) covalent geometry : angle 0.71202 / 0.41 (28328) hydrogen bonds : bond 0.11813 / 7.85 ( 884) hydrogen bonds : angle 4.98864 / 3.51 ( 2612) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 268 time to evaluate : 0.755 Fit side-chains REVERT: A 102 TYR cc_start: 0.5768 (OUTLIER) cc_final: 0.4470 (m-80) REVERT: B 102 TYR cc_start: 0.5845 (OUTLIER) cc_final: 0.4402 (m-10) REVERT: B 419 MET cc_start: 0.5738 (OUTLIER) cc_final: 0.5423 (mtt) REVERT: C 102 TYR cc_start: 0.5992 (OUTLIER) cc_final: 0.4707 (m-80) REVERT: D 102 TYR cc_start: 0.5810 (OUTLIER) cc_final: 0.4578 (m-80) outliers start: 24 outliers final: 2 residues processed: 276 average time/residue: 0.4470 time to fit residues: 143.1949 Evaluate side-chains 192 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 185 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 TYR Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain D residue 102 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 30.0000 chunk 247 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 HIS ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN B 253 HIS ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.202041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.161099 restraints weight = 37549.689| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 6.80 r_work: 0.3225 rms_B_bonded: 5.74 restraints_weight: 2.0000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20896 Z= 0.180 Angle : 0.619 7.380 28328 Z= 0.312 Chirality : 0.044 0.195 3040 Planarity : 0.004 0.049 3612 Dihedral : 4.853 90.370 2806 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.59 % Allowed : 10.49 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.17), residues: 2476 helix: 1.18 (0.15), residues: 1244 sheet: -1.56 (0.35), residues: 200 loop : -1.20 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 402 TYR 0.020 0.002 TYR D 600 PHE 0.014 0.002 PHE A 433 TRP 0.039 0.002 TRP D 106 HIS 0.005 0.001 HIS D 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (20896) covalent geometry : angle 0.61879 / 0.31 (28328) hydrogen bonds : bond 0.04240 / 2.71 ( 884) hydrogen bonds : angle 4.33553 / 3.07 ( 2612) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 203 time to evaluate : 0.601 Fit side-chains REVERT: A 115 VAL cc_start: 0.6281 (t) cc_final: 0.5889 (m) REVERT: A 205 HIS cc_start: 0.7400 (m-70) cc_final: 0.7178 (m170) REVERT: A 228 ASN cc_start: 0.8385 (t0) cc_final: 0.8173 (t0) REVERT: A 244 MET cc_start: 0.7732 (ppp) cc_final: 0.7404 (ppp) REVERT: B 205 HIS cc_start: 0.7703 (m170) cc_final: 0.7496 (m170) REVERT: B 244 MET cc_start: 0.7793 (ppp) cc_final: 0.7371 (ppp) REVERT: C 61 ASN cc_start: 0.7930 (m-40) cc_final: 0.7639 (t0) REVERT: C 387 LYS cc_start: 0.8171 (ptpt) cc_final: 0.7917 (pttt) REVERT: C 422 LYS cc_start: 0.8060 (ttmm) cc_final: 0.7812 (ttpp) REVERT: D 114 VAL cc_start: 0.7066 (m) cc_final: 0.6796 (m) REVERT: D 244 MET cc_start: 0.7705 (ppp) cc_final: 0.7422 (ppp) REVERT: D 402 ARG cc_start: 0.8343 (ttp-110) cc_final: 0.8069 (mtm110) outliers start: 34 outliers final: 8 residues processed: 214 average time/residue: 0.4546 time to fit residues: 113.8478 Evaluate side-chains 190 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 182 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain F residue 333 MET Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 606 MET Chi-restraints excluded: chain D residue 469 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 90 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 151 optimal weight: 7.9990 chunk 129 optimal weight: 0.7980 chunk 6 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 122 optimal weight: 0.0370 chunk 213 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 9.9990 chunk 60 optimal weight: 20.0000 overall best weight: 2.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 HIS B 178 HIS ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 HIS D 178 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.197668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.155630 restraints weight = 34724.936| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 6.63 r_work: 0.3138 rms_B_bonded: 5.20 restraints_weight: 2.0000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 20896 Z= 0.285 Angle : 0.700 7.535 28328 Z= 0.358 Chirality : 0.049 0.265 3040 Planarity : 0.005 0.047 3612 Dihedral : 4.868 27.238 2792 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.80 % Allowed : 11.38 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.17), residues: 2476 helix: 0.89 (0.15), residues: 1240 sheet: -1.24 (0.35), residues: 220 loop : -1.38 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 586 TYR 0.028 0.002 TYR D 600 PHE 0.021 0.002 PHE A 179 TRP 0.037 0.002 TRP A 106 HIS 0.007 0.002 HIS B 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00680 / 0.28 (20896) covalent geometry : angle 0.70011 / 0.36 (28328) hydrogen bonds : bond 0.04939 / 3.14 ( 884) hydrogen bonds : angle 4.40651 / 3.13 ( 2612) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 198 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 115 VAL cc_start: 0.6583 (t) cc_final: 0.6230 (m) REVERT: A 160 TRP cc_start: 0.6768 (OUTLIER) cc_final: 0.6221 (t60) REVERT: A 228 ASN cc_start: 0.8422 (t0) cc_final: 0.8158 (t0) REVERT: A 244 MET cc_start: 0.7745 (ppp) cc_final: 0.7442 (ppp) REVERT: A 514 TYR cc_start: 0.8341 (OUTLIER) cc_final: 0.8002 (m-80) REVERT: G 333 MET cc_start: 0.6611 (mmp) cc_final: 0.6301 (mmp) REVERT: B 220 PHE cc_start: 0.7865 (t80) cc_final: 0.7420 (t80) REVERT: B 244 MET cc_start: 0.7917 (ppp) cc_final: 0.7535 (ppp) REVERT: B 371 ARG cc_start: 0.8363 (ptm-80) cc_final: 0.8081 (ptm-80) REVERT: B 416 MET cc_start: 0.6004 (tpp) cc_final: 0.5633 (tpt) REVERT: B 422 LYS cc_start: 0.8327 (ttmm) cc_final: 0.7836 (ttpp) REVERT: B 448 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7653 (mtm) REVERT: B 514 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.7954 (m-80) REVERT: C 115 VAL cc_start: 0.6216 (t) cc_final: 0.5896 (m) REVERT: C 182 TRP cc_start: 0.8258 (OUTLIER) cc_final: 0.7840 (p90) REVERT: C 402 ARG cc_start: 0.8361 (ttp-110) cc_final: 0.8131 (mtm110) REVERT: C 422 LYS cc_start: 0.8274 (ttmm) cc_final: 0.7897 (ttpp) REVERT: C 514 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.8002 (m-80) REVERT: D 115 VAL cc_start: 0.6515 (t) cc_final: 0.6160 (m) REVERT: D 182 TRP cc_start: 0.8348 (OUTLIER) cc_final: 0.7921 (p90) REVERT: D 244 MET cc_start: 0.7736 (ppp) cc_final: 0.7460 (ppp) REVERT: D 402 ARG cc_start: 0.8369 (ttp-110) cc_final: 0.8111 (mtm110) REVERT: D 514 TYR cc_start: 0.8298 (OUTLIER) cc_final: 0.7953 (m-80) outliers start: 60 outliers final: 21 residues processed: 227 average time/residue: 0.4297 time to fit residues: 115.1599 Evaluate side-chains 209 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 TRP Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain F residue 333 MET Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 514 TYR Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 182 TRP Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 514 TYR Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 514 TYR Chi-restraints excluded: chain D residue 515 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 173 optimal weight: 0.5980 chunk 38 optimal weight: 0.0980 chunk 37 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 230 optimal weight: 0.4980 chunk 149 optimal weight: 0.6980 chunk 66 optimal weight: 7.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 260 GLN C 267 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.201879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.159860 restraints weight = 48194.850| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 2.66 r_work: 0.3467 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20896 Z= 0.119 Angle : 0.548 9.815 28328 Z= 0.278 Chirality : 0.041 0.141 3040 Planarity : 0.004 0.044 3612 Dihedral : 4.290 21.227 2792 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.54 % Allowed : 14.55 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.17), residues: 2476 helix: 1.22 (0.15), residues: 1244 sheet: -1.55 (0.33), residues: 228 loop : -1.35 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 402 TYR 0.025 0.001 TYR C 600 PHE 0.016 0.001 PHE A 179 TRP 0.022 0.002 TRP B 182 HIS 0.008 0.001 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (20896) covalent geometry : angle 0.54823 / 0.28 (28328) hydrogen bonds : bond 0.03657 / 2.32 ( 884) hydrogen bonds : angle 3.94411 / 2.80 ( 2612) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 VAL cc_start: 0.6832 (t) cc_final: 0.6580 (m) REVERT: A 182 TRP cc_start: 0.8185 (OUTLIER) cc_final: 0.7802 (p90) REVERT: A 228 ASN cc_start: 0.8342 (t0) cc_final: 0.8140 (t0) REVERT: G 333 MET cc_start: 0.5550 (mmp) cc_final: 0.4941 (mmp) REVERT: B 114 VAL cc_start: 0.7112 (m) cc_final: 0.6770 (m) REVERT: B 264 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8285 (mp) REVERT: B 416 MET cc_start: 0.5510 (tpp) cc_final: 0.5290 (tpt) REVERT: C 115 VAL cc_start: 0.6767 (t) cc_final: 0.6468 (m) REVERT: C 182 TRP cc_start: 0.8101 (OUTLIER) cc_final: 0.7853 (p90) REVERT: D 115 VAL cc_start: 0.6913 (t) cc_final: 0.6628 (m) REVERT: D 182 TRP cc_start: 0.8104 (OUTLIER) cc_final: 0.7862 (p90) outliers start: 33 outliers final: 14 residues processed: 204 average time/residue: 0.3904 time to fit residues: 94.6278 Evaluate side-chains 185 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TRP Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain F residue 333 MET Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain C residue 182 TRP Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 483 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 202 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 chunk 211 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 247 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 225 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.197450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.154759 restraints weight = 41393.684| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 7.19 r_work: 0.3145 rms_B_bonded: 5.10 restraints_weight: 2.0000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 20896 Z= 0.264 Angle : 0.673 10.237 28328 Z= 0.341 Chirality : 0.047 0.218 3040 Planarity : 0.004 0.053 3612 Dihedral : 4.835 38.384 2792 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.52 % Allowed : 15.44 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.17), residues: 2476 helix: 0.90 (0.15), residues: 1240 sheet: -1.61 (0.33), residues: 228 loop : -1.53 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 402 TYR 0.029 0.002 TYR C 600 PHE 0.020 0.002 PHE C 179 TRP 0.035 0.002 TRP C 106 HIS 0.007 0.001 HIS B 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.26 (20896) covalent geometry : angle 0.67279 / 0.34 (28328) hydrogen bonds : bond 0.04677 / 2.96 ( 884) hydrogen bonds : angle 4.22825 / 3.01 ( 2612) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 173 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 VAL cc_start: 0.6530 (t) cc_final: 0.6202 (m) REVERT: A 182 TRP cc_start: 0.8482 (OUTLIER) cc_final: 0.8059 (p90) REVERT: A 228 ASN cc_start: 0.8461 (t0) cc_final: 0.8165 (t0) REVERT: A 514 TYR cc_start: 0.8362 (OUTLIER) cc_final: 0.7886 (m-80) REVERT: G 333 MET cc_start: 0.6640 (mmp) cc_final: 0.6419 (mmp) REVERT: B 220 PHE cc_start: 0.7814 (t80) cc_final: 0.7424 (t80) REVERT: B 416 MET cc_start: 0.5947 (tpp) cc_final: 0.5636 (tpt) REVERT: B 448 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7720 (mtm) REVERT: B 514 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.7920 (m-80) REVERT: C 115 VAL cc_start: 0.6362 (t) cc_final: 0.6059 (m) REVERT: C 178 HIS cc_start: 0.6341 (t-170) cc_final: 0.5961 (t-90) REVERT: C 182 TRP cc_start: 0.8387 (OUTLIER) cc_final: 0.8163 (p90) REVERT: C 228 ASN cc_start: 0.7853 (t0) cc_final: 0.7544 (t0) REVERT: D 114 VAL cc_start: 0.7205 (m) cc_final: 0.6887 (m) REVERT: D 115 VAL cc_start: 0.6526 (t) cc_final: 0.6194 (m) REVERT: D 182 TRP cc_start: 0.8422 (OUTLIER) cc_final: 0.8174 (p90) REVERT: D 514 TYR cc_start: 0.8372 (OUTLIER) cc_final: 0.7833 (m-80) outliers start: 54 outliers final: 24 residues processed: 207 average time/residue: 0.4257 time to fit residues: 104.6472 Evaluate side-chains 204 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TRP Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain F residue 333 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 514 TYR Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 605 TYR Chi-restraints excluded: chain C residue 182 TRP Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 514 TYR Chi-restraints excluded: chain D residue 515 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 20.0000 chunk 204 optimal weight: 8.9990 chunk 77 optimal weight: 0.0980 chunk 129 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 chunk 149 optimal weight: 0.4980 chunk 11 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 260 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.199969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.157395 restraints weight = 48787.128| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.59 r_work: 0.3478 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20896 Z= 0.145 Angle : 0.580 9.274 28328 Z= 0.292 Chirality : 0.042 0.143 3040 Planarity : 0.004 0.042 3612 Dihedral : 4.517 38.674 2792 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.10 % Allowed : 16.65 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.17), residues: 2476 helix: 1.07 (0.15), residues: 1244 sheet: -1.60 (0.33), residues: 228 loop : -1.44 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 402 TYR 0.026 0.001 TYR A 600 PHE 0.014 0.001 PHE D 179 TRP 0.025 0.001 TRP C 106 HIS 0.005 0.001 HIS D 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (20896) covalent geometry : angle 0.57999 / 0.29 (28328) hydrogen bonds : bond 0.03866 / 2.45 ( 884) hydrogen bonds : angle 3.98936 / 2.83 ( 2612) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 VAL cc_start: 0.6800 (t) cc_final: 0.6519 (m) REVERT: A 228 ASN cc_start: 0.8456 (t0) cc_final: 0.8249 (t0) REVERT: A 514 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.7918 (m-80) REVERT: G 333 MET cc_start: 0.6251 (mmp) cc_final: 0.5887 (mmp) REVERT: B 114 VAL cc_start: 0.7062 (m) cc_final: 0.6717 (m) REVERT: B 178 HIS cc_start: 0.6918 (t-170) cc_final: 0.6595 (t-90) REVERT: B 264 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8370 (mp) REVERT: B 416 MET cc_start: 0.5436 (tpp) cc_final: 0.5230 (tpt) REVERT: B 448 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7558 (mtm) REVERT: C 115 VAL cc_start: 0.6747 (t) cc_final: 0.6464 (m) REVERT: D 115 VAL cc_start: 0.6826 (t) cc_final: 0.6571 (m) REVERT: D 182 TRP cc_start: 0.8251 (OUTLIER) cc_final: 0.8025 (p90) outliers start: 45 outliers final: 23 residues processed: 204 average time/residue: 0.4130 time to fit residues: 100.8862 Evaluate side-chains 201 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain F residue 333 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 515 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 227 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 164 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 242 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 140 optimal weight: 6.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.199351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.157460 restraints weight = 42540.451| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 7.25 r_work: 0.3218 rms_B_bonded: 5.33 restraints_weight: 2.0000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20896 Z= 0.169 Angle : 0.599 10.234 28328 Z= 0.302 Chirality : 0.042 0.145 3040 Planarity : 0.004 0.042 3612 Dihedral : 4.484 36.424 2792 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.91 % Allowed : 17.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.17), residues: 2476 helix: 1.04 (0.15), residues: 1244 sheet: -1.64 (0.33), residues: 228 loop : -1.47 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 402 TYR 0.027 0.002 TYR A 600 PHE 0.016 0.002 PHE D 179 TRP 0.027 0.001 TRP C 106 HIS 0.005 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (20896) covalent geometry : angle 0.59896 / 0.30 (28328) hydrogen bonds : bond 0.04037 / 2.56 ( 884) hydrogen bonds : angle 4.00530 / 2.85 ( 2612) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 178 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 VAL cc_start: 0.6348 (t) cc_final: 0.6006 (m) REVERT: A 228 ASN cc_start: 0.8506 (t0) cc_final: 0.8182 (t0) REVERT: A 514 TYR cc_start: 0.8390 (OUTLIER) cc_final: 0.8013 (m-80) REVERT: G 333 MET cc_start: 0.6690 (mmp) cc_final: 0.6478 (mmp) REVERT: B 114 VAL cc_start: 0.6727 (m) cc_final: 0.6386 (m) REVERT: B 178 HIS cc_start: 0.6757 (t-170) cc_final: 0.6371 (t-90) REVERT: B 182 TRP cc_start: 0.8315 (OUTLIER) cc_final: 0.7855 (p90) REVERT: B 220 PHE cc_start: 0.7761 (t80) cc_final: 0.7491 (t80) REVERT: B 264 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.8087 (mp) REVERT: B 416 MET cc_start: 0.5734 (tpp) cc_final: 0.5448 (tpt) REVERT: C 115 VAL cc_start: 0.6309 (t) cc_final: 0.5982 (m) REVERT: D 114 VAL cc_start: 0.7114 (m) cc_final: 0.6776 (m) REVERT: D 115 VAL cc_start: 0.6503 (t) cc_final: 0.6146 (m) REVERT: D 178 HIS cc_start: 0.6605 (t-170) cc_final: 0.6180 (t-90) REVERT: D 514 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.7941 (m-80) outliers start: 41 outliers final: 22 residues processed: 203 average time/residue: 0.4252 time to fit residues: 101.9028 Evaluate side-chains 194 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain F residue 333 MET Chi-restraints excluded: chain B residue 182 TRP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 514 TYR Chi-restraints excluded: chain D residue 515 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 70 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 3 optimal weight: 0.0670 chunk 218 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 161 optimal weight: 0.0270 chunk 133 optimal weight: 10.0000 chunk 245 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 chunk 86 optimal weight: 20.0000 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.202046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.155601 restraints weight = 56539.854| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.96 r_work: 0.3396 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20896 Z= 0.118 Angle : 0.559 10.052 28328 Z= 0.281 Chirality : 0.040 0.138 3040 Planarity : 0.004 0.042 3612 Dihedral : 4.171 25.532 2792 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.87 % Allowed : 17.96 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.17), residues: 2476 helix: 1.19 (0.15), residues: 1248 sheet: -1.49 (0.33), residues: 224 loop : -1.38 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 402 TYR 0.026 0.001 TYR A 600 PHE 0.011 0.001 PHE C 179 TRP 0.021 0.001 TRP C 106 HIS 0.004 0.001 HIS C 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (20896) covalent geometry : angle 0.55904 / 0.28 (28328) hydrogen bonds : bond 0.03578 / 2.27 ( 884) hydrogen bonds : angle 3.87163 / 2.75 ( 2612) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 186 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 VAL cc_start: 0.6756 (t) cc_final: 0.6421 (m) REVERT: A 228 ASN cc_start: 0.8498 (t0) cc_final: 0.8268 (t0) REVERT: G 333 MET cc_start: 0.6148 (mmp) cc_final: 0.5827 (mmp) REVERT: B 114 VAL cc_start: 0.7075 (m) cc_final: 0.6700 (m) REVERT: B 264 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8320 (mp) REVERT: B 416 MET cc_start: 0.5487 (tpp) cc_final: 0.5283 (tpt) REVERT: C 115 VAL cc_start: 0.6818 (t) cc_final: 0.6472 (m) REVERT: D 114 VAL cc_start: 0.7430 (m) cc_final: 0.7051 (m) REVERT: D 115 VAL cc_start: 0.6917 (t) cc_final: 0.6607 (m) REVERT: D 178 HIS cc_start: 0.6543 (t-170) cc_final: 0.6328 (t-90) outliers start: 40 outliers final: 22 residues processed: 213 average time/residue: 0.4330 time to fit residues: 109.0403 Evaluate side-chains 198 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain E residue 333 MET Chi-restraints excluded: chain F residue 333 MET Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 515 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 59 optimal weight: 0.9990 chunk 226 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 197 optimal weight: 8.9990 chunk 159 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 220 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 HIS ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.198897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.158787 restraints weight = 51147.584| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.79 r_work: 0.3397 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3362 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20896 Z= 0.192 Angle : 0.623 10.326 28328 Z= 0.314 Chirality : 0.044 0.155 3040 Planarity : 0.004 0.043 3612 Dihedral : 4.419 24.697 2792 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.68 % Allowed : 18.66 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.17), residues: 2476 helix: 1.04 (0.15), residues: 1244 sheet: -1.39 (0.29), residues: 296 loop : -1.42 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 586 TYR 0.027 0.002 TYR C 600 PHE 0.016 0.002 PHE A 179 TRP 0.030 0.002 TRP B 106 HIS 0.005 0.001 HIS C 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 (20896) covalent geometry : angle 0.62326 / 0.31 (28328) hydrogen bonds : bond 0.04152 / 2.63 ( 884) hydrogen bonds : angle 4.06644 / 2.89 ( 2612) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 178 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 VAL cc_start: 0.7454 (m) cc_final: 0.7251 (m) REVERT: A 115 VAL cc_start: 0.6770 (t) cc_final: 0.6359 (m) REVERT: A 514 TYR cc_start: 0.8344 (OUTLIER) cc_final: 0.7858 (m-80) REVERT: B 264 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8381 (mp) REVERT: B 416 MET cc_start: 0.5528 (tpp) cc_final: 0.5279 (tpt) REVERT: C 115 VAL cc_start: 0.6526 (t) cc_final: 0.6147 (m) REVERT: D 114 VAL cc_start: 0.7463 (m) cc_final: 0.7094 (m) REVERT: D 115 VAL cc_start: 0.7029 (t) cc_final: 0.6716 (m) REVERT: D 178 HIS cc_start: 0.6716 (t-170) cc_final: 0.6426 (t-90) outliers start: 36 outliers final: 24 residues processed: 202 average time/residue: 0.3918 time to fit residues: 94.5448 Evaluate side-chains 191 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain F residue 333 MET Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 182 TRP Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 515 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 3 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 chunk 144 optimal weight: 6.9990 chunk 238 optimal weight: 4.9990 chunk 228 optimal weight: 0.4980 chunk 137 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 223 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.198993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.156892 restraints weight = 46193.213| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.48 r_work: 0.3433 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20896 Z= 0.179 Angle : 0.623 10.482 28328 Z= 0.314 Chirality : 0.043 0.160 3040 Planarity : 0.004 0.042 3612 Dihedral : 4.433 24.298 2792 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.68 % Allowed : 18.94 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.17), residues: 2476 helix: 1.03 (0.15), residues: 1244 sheet: -1.44 (0.29), residues: 296 loop : -1.46 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 402 TYR 0.027 0.002 TYR A 600 PHE 0.015 0.002 PHE C 179 TRP 0.032 0.001 TRP B 106 HIS 0.005 0.001 HIS B 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (20896) covalent geometry : angle 0.62252 / 0.31 (28328) hydrogen bonds : bond 0.04103 / 2.60 ( 884) hydrogen bonds : angle 4.05628 / 2.88 ( 2612) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4952 Ramachandran restraints generated. 2476 Oldfield, 0 Emsley, 2476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 VAL cc_start: 0.7397 (m) cc_final: 0.7018 (m) REVERT: A 115 VAL cc_start: 0.6600 (t) cc_final: 0.6171 (m) REVERT: B 182 TRP cc_start: 0.8196 (OUTLIER) cc_final: 0.7898 (p90) REVERT: B 264 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8348 (mp) REVERT: C 115 VAL cc_start: 0.6403 (t) cc_final: 0.6024 (m) REVERT: D 114 VAL cc_start: 0.7414 (m) cc_final: 0.7053 (m) REVERT: D 115 VAL cc_start: 0.6882 (t) cc_final: 0.6578 (m) REVERT: D 178 HIS cc_start: 0.6692 (t-170) cc_final: 0.6393 (t-90) outliers start: 36 outliers final: 25 residues processed: 197 average time/residue: 0.4168 time to fit residues: 96.9964 Evaluate side-chains 193 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain F residue 333 MET Chi-restraints excluded: chain B residue 182 TRP Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 182 TRP Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 515 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 231 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 205 optimal weight: 3.9990 chunk 239 optimal weight: 0.2980 chunk 18 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.199242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.168948 restraints weight = 31147.612| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 3.18 r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4134 r_free = 0.4134 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4134 r_free = 0.4134 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20896 Z= 0.163 Angle : 0.611 10.434 28328 Z= 0.307 Chirality : 0.043 0.185 3040 Planarity : 0.004 0.043 3612 Dihedral : 4.363 20.910 2792 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.63 % Allowed : 19.26 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.17), residues: 2476 helix: 1.06 (0.15), residues: 1244 sheet: -1.42 (0.29), residues: 296 loop : -1.43 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 402 TYR 0.027 0.002 TYR A 600 PHE 0.014 0.001 PHE C 179 TRP 0.034 0.001 TRP B 106 HIS 0.004 0.001 HIS C 478 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (20896) covalent geometry : angle 0.61113 / 0.31 (28328) hydrogen bonds : bond 0.03985 / 2.52 ( 884) hydrogen bonds : angle 4.04715 / 2.87 ( 2612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5227.52 seconds wall clock time: 90 minutes 17.15 seconds (5417.15 seconds total)