Starting phenix.real_space_refine on Sun Aug 24 14:23:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q13_13753/08_2025/7q13_13753.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q13_13753/08_2025/7q13_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7q13_13753/08_2025/7q13_13753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q13_13753/08_2025/7q13_13753.map" model { file = "/net/cci-nas-00/data/ceres_data/7q13_13753/08_2025/7q13_13753.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q13_13753/08_2025/7q13_13753.cif" } 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-2.0-5787/lib/python3.9/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: 8.74, per 1000 atoms: 0.43 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: 1.92 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.83 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: 3.86 Time building geometry restraints manager: 2.58 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: 27439 1.84 - 3.68: 676 3.68 - 5.52: 159 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 - 29.57: 11835 29.57 - 59.14: 527 59.14 - 88.72: 57 88.72 - 118.29: 49 118.29 - 147.86: 28 Dihedral angle restraints: 12496 sinusoidal: 5240 harmonic: 7256 Sorted by residual: dihedral pdb=" C3 G6P C 801 " pdb=" C1 G6P C 801 " pdb=" C2 G6P C 801 " pdb=" O1 G6P C 801 " ideal model delta sinusoidal sigma weight residual 74.65 -73.21 147.86 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" C3 G6P D 801 " pdb=" C1 G6P D 801 " pdb=" C2 G6P D 801 " pdb=" O1 G6P D 801 " ideal model delta sinusoidal sigma weight residual 74.65 -73.18 147.83 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" C3 G6P A 801 " pdb=" C1 G6P A 801 " pdb=" C2 G6P A 801 " pdb=" O1 G6P A 801 " ideal model delta sinusoidal sigma weight residual 74.65 -73.18 147.83 1 3.00e+01 1.11e-03 1.97e+01 ... (remaining 12493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.020: 3024 1.020 - 2.039: 0 2.039 - 3.059: 0 3.059 - 4.078: 0 4.078 - 5.098: 16 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: 0.09 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 25.340 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 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= 0.242 Angle : 0.722 9.208 28328 Z= 0.413 Chirality : 0.350 5.098 3040 Planarity : 0.004 0.055 3612 Dihedral : 19.553 147.861 7832 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 aren 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 covalent geometry : bond 0.00411 (20896) covalent geometry : angle 0.72184 (28328) hydrogen bonds : bond 0.11813 ( 884) hydrogen bonds : angle 4.98864 ( 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 : 0.736 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: 0.5555 time to fit residues: 176.7657 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 : 0.793 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 205 HIS A 253 HIS 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.201895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.162075 restraints weight = 37379.419| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 6.08 r_work: 0.3241 rms_B_bonded: 5.69 restraints_weight: 2.0000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20896 Z= 0.182 Angle : 0.654 8.098 28328 Z= 0.321 Chirality : 0.045 0.187 3040 Planarity : 0.004 0.049 3612 Dihedral : 8.416 89.599 3082 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.73 % Allowed : 10.31 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.17), residues: 2476 helix: 1.17 (0.15), residues: 1244 sheet: -1.55 (0.35), residues: 200 loop : -1.20 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 586 TYR 0.021 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 covalent geometry : bond 0.00430 (20896) covalent geometry : angle 0.65435 (28328) hydrogen bonds : bond 0.04200 ( 884) hydrogen bonds : angle 4.32798 ( 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 244 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: A 115 VAL cc_start: 0.6360 (t) cc_final: 0.5960 (m) REVERT: A 205 HIS cc_start: 0.7440 (m-70) cc_final: 0.7227 (m170) REVERT: A 220 PHE cc_start: 0.7902 (t80) cc_final: 0.7629 (t80) REVERT: A 228 ASN cc_start: 0.8398 (t0) cc_final: 0.8183 (t0) REVERT: A 244 MET cc_start: 0.7728 (ppp) cc_final: 0.7399 (ppp) REVERT: A 265 GLU cc_start: 0.7085 (pm20) cc_final: 0.6847 (mp0) REVERT: B 205 HIS cc_start: 0.7703 (m170) cc_final: 0.7503 (m170) REVERT: B 244 MET cc_start: 0.7778 (ppp) cc_final: 0.7356 (ppp) REVERT: C 422 LYS cc_start: 0.8055 (ttmm) cc_final: 0.7826 (ttpp) REVERT: D 114 VAL cc_start: 0.7068 (m) cc_final: 0.6795 (m) REVERT: D 205 HIS cc_start: 0.7892 (m90) cc_final: 0.7671 (m170) REVERT: D 244 MET cc_start: 0.7580 (ppp) cc_final: 0.7290 (ppp) REVERT: D 402 ARG cc_start: 0.8332 (ttp-110) cc_final: 0.8065 (mtm110) outliers start: 37 outliers final: 10 residues processed: 219 average time/residue: 0.5611 time to fit residues: 142.1244 Evaluate side-chains 190 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 SER 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 606 MET Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 606 MET Chi-restraints excluded: chain D residue 483 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: 0.2980 chunk 151 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 122 optimal weight: 0.1980 chunk 213 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 60 optimal weight: 30.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS B 178 HIS ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS C 178 HIS C 267 GLN C 297 HIS D 178 HIS ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.200506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.159030 restraints weight = 35432.290| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 6.67 r_work: 0.3129 rms_B_bonded: 5.98 restraints_weight: 2.0000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 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 = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2006 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= 0.180 Angle : 0.597 7.556 28328 Z= 0.304 Chirality : 0.043 0.155 3040 Planarity : 0.004 0.046 3612 Dihedral : 6.580 89.223 3069 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.01 % Allowed : 11.89 % Favored : 86.10 % 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 aren not related in a simple way. whole: -0.03 (0.17), residues: 2476 helix: 1.17 (0.15), residues: 1244 sheet: -1.19 (0.34), residues: 220 loop : -1.23 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 402 TYR 0.026 0.002 TYR D 600 PHE 0.016 0.002 PHE A 179 TRP 0.036 0.002 TRP A 106 HIS 0.004 0.001 HIS C 478 Details of bonding type rmsd covalent geometry : bond 0.00427 (20896) covalent geometry : angle 0.59734 (28328) hydrogen bonds : bond 0.04189 ( 884) hydrogen bonds : angle 4.11074 ( 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 238 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 195 time to evaluate : 0.856 Fit side-chains REVERT: A 115 VAL cc_start: 0.6586 (t) cc_final: 0.6270 (m) REVERT: A 220 PHE cc_start: 0.7918 (t80) cc_final: 0.7553 (t80) REVERT: A 228 ASN cc_start: 0.8457 (t0) cc_final: 0.8227 (t0) REVERT: A 244 MET cc_start: 0.7641 (ppp) cc_final: 0.7437 (ppp) REVERT: G 333 MET cc_start: 0.6359 (mmp) cc_final: 0.6070 (mmp) REVERT: B 114 VAL cc_start: 0.7005 (m) cc_final: 0.6680 (m) REVERT: B 244 MET cc_start: 0.7867 (ppp) cc_final: 0.7612 (ppp) REVERT: B 371 ARG cc_start: 0.8336 (ptm-80) cc_final: 0.7955 (ptm-80) REVERT: B 422 LYS cc_start: 0.8423 (ttmm) cc_final: 0.7875 (ttpp) REVERT: C 115 VAL cc_start: 0.6167 (t) cc_final: 0.5907 (m) REVERT: C 265 GLU cc_start: 0.7410 (pm20) cc_final: 0.7067 (mp0) REVERT: C 402 ARG cc_start: 0.8384 (ttp-110) cc_final: 0.8128 (mtm110) REVERT: C 422 LYS cc_start: 0.8200 (ttmm) cc_final: 0.7810 (ttpp) REVERT: D 114 VAL cc_start: 0.7199 (m) cc_final: 0.6917 (m) REVERT: D 115 VAL cc_start: 0.6483 (t) cc_final: 0.6167 (m) REVERT: D 182 TRP cc_start: 0.8366 (OUTLIER) cc_final: 0.7976 (p90) REVERT: D 402 ARG cc_start: 0.8380 (ttp-110) cc_final: 0.8114 (mtm110) outliers start: 43 outliers final: 18 residues processed: 215 average time/residue: 0.4791 time to fit residues: 120.5854 Evaluate side-chains 200 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 515 THR 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 260 GLN 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 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 427 MET Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 483 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 173 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 152 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 118 optimal weight: 0.0980 chunk 19 optimal weight: 0.0170 chunk 30 optimal weight: 1.9990 chunk 230 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 overall best weight: 0.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 ASN B 260 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.202420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.159742 restraints weight = 47690.358| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 2.51 r_work: 0.3487 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 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 = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2128 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= 0.117 Angle : 0.537 9.855 28328 Z= 0.271 Chirality : 0.040 0.138 3040 Planarity : 0.003 0.043 3612 Dihedral : 5.796 88.465 3068 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.01 % Allowed : 13.99 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.17), residues: 2476 helix: 1.34 (0.15), residues: 1248 sheet: -1.49 (0.36), residues: 200 loop : -1.29 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 402 TYR 0.026 0.001 TYR C 600 PHE 0.011 0.001 PHE A 179 TRP 0.024 0.001 TRP C 106 HIS 0.004 0.001 HIS B 541 Details of bonding type rmsd covalent geometry : bond 0.00266 (20896) covalent geometry : angle 0.53664 (28328) hydrogen bonds : bond 0.03597 ( 884) hydrogen bonds : angle 3.86772 ( 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 237 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 194 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 VAL cc_start: 0.6885 (t) cc_final: 0.6648 (m) REVERT: A 182 TRP cc_start: 0.8223 (OUTLIER) cc_final: 0.7831 (p90) REVERT: A 205 HIS cc_start: 0.7645 (m170) cc_final: 0.7408 (m170) REVERT: A 228 ASN cc_start: 0.8393 (t0) cc_final: 0.8188 (t0) REVERT: G 333 MET cc_start: 0.5558 (mmp) cc_final: 0.5016 (mmp) REVERT: B 114 VAL cc_start: 0.7071 (m) cc_final: 0.6750 (m) REVERT: B 178 HIS cc_start: 0.7161 (t-170) cc_final: 0.6957 (t-90) REVERT: B 205 HIS cc_start: 0.7807 (m170) cc_final: 0.7583 (m170) REVERT: B 264 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8271 (mp) REVERT: B 416 MET cc_start: 0.5326 (tpp) cc_final: 0.5064 (tpt) REVERT: C 115 VAL cc_start: 0.6681 (t) cc_final: 0.6423 (m) REVERT: C 422 LYS cc_start: 0.7932 (ttmm) cc_final: 0.7719 (ttpp) REVERT: D 115 VAL cc_start: 0.6850 (t) cc_final: 0.6618 (m) REVERT: D 352 LEU cc_start: 0.8325 (mp) cc_final: 0.8099 (mp) outliers start: 43 outliers final: 14 residues processed: 212 average time/residue: 0.4726 time to fit residues: 116.8621 Evaluate side-chains 194 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 427 MET Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 561 ASP 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 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 469 SER Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 515 THR 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: 0.8980 chunk 207 optimal weight: 8.9990 chunk 145 optimal weight: 10.0000 chunk 211 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 247 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 225 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 9 optimal weight: 20.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.196435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.152971 restraints weight = 40165.925| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 7.84 r_work: 0.3088 rms_B_bonded: 5.23 restraints_weight: 2.0000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 20896 Z= 0.311 Angle : 0.707 9.761 28328 Z= 0.363 Chirality : 0.049 0.289 3040 Planarity : 0.005 0.053 3612 Dihedral : 6.548 87.826 3068 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 2.61 % Allowed : 15.21 % Favored : 82.18 % 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 aren not related in a simple way. whole: -0.42 (0.17), residues: 2476 helix: 0.84 (0.15), residues: 1240 sheet: -1.31 (0.34), residues: 220 loop : -1.42 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 402 TYR 0.029 0.002 TYR A 600 PHE 0.021 0.002 PHE A 318 TRP 0.034 0.002 TRP B 106 HIS 0.008 0.002 HIS A 478 Details of bonding type rmsd covalent geometry : bond 0.00745 (20896) covalent geometry : angle 0.70667 (28328) hydrogen bonds : bond 0.04960 ( 884) hydrogen bonds : angle 4.36014 ( 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 234 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 178 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 VAL cc_start: 0.6504 (t) cc_final: 0.6164 (m) REVERT: A 182 TRP cc_start: 0.8509 (OUTLIER) cc_final: 0.7965 (p90) REVERT: A 228 ASN cc_start: 0.8436 (t0) cc_final: 0.8139 (t0) REVERT: G 333 MET cc_start: 0.6731 (mmp) cc_final: 0.6317 (mmp) REVERT: B 416 MET cc_start: 0.5919 (tpp) cc_final: 0.5597 (tpt) REVERT: B 448 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7688 (mtm) REVERT: B 514 TYR cc_start: 0.8297 (OUTLIER) cc_final: 0.7801 (m-80) REVERT: C 115 VAL cc_start: 0.6470 (t) cc_final: 0.6126 (m) REVERT: C 228 ASN cc_start: 0.7868 (t0) cc_final: 0.7614 (t0) REVERT: C 422 LYS cc_start: 0.8264 (ttmm) cc_final: 0.7842 (ttpp) REVERT: D 115 VAL cc_start: 0.6534 (t) cc_final: 0.6221 (m) REVERT: D 514 TYR cc_start: 0.8275 (OUTLIER) cc_final: 0.7743 (m-80) outliers start: 56 outliers final: 22 residues processed: 210 average time/residue: 0.4688 time to fit residues: 115.4618 Evaluate side-chains 199 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TRP 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 427 MET 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 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 265 GLU 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: 0.0050 chunk 204 optimal weight: 9.9990 chunk 77 optimal weight: 0.2980 chunk 129 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 166 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.201039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.159580 restraints weight = 47974.911| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 2.67 r_work: 0.3445 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2574 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= 0.117 Angle : 0.563 10.629 28328 Z= 0.283 Chirality : 0.041 0.139 3040 Planarity : 0.004 0.042 3612 Dihedral : 5.951 89.157 3068 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.82 % Allowed : 16.56 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.17), residues: 2476 helix: 1.18 (0.15), residues: 1244 sheet: -1.58 (0.33), residues: 228 loop : -1.39 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 402 TYR 0.025 0.001 TYR C 600 PHE 0.013 0.001 PHE B 179 TRP 0.019 0.001 TRP B 106 HIS 0.003 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00265 (20896) covalent geometry : angle 0.56257 (28328) hydrogen bonds : bond 0.03673 ( 884) hydrogen bonds : angle 3.93192 ( 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 213 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 174 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 VAL cc_start: 0.6741 (t) cc_final: 0.6484 (m) REVERT: A 182 TRP cc_start: 0.8347 (OUTLIER) cc_final: 0.7886 (p90) REVERT: A 228 ASN cc_start: 0.8409 (t0) cc_final: 0.8166 (t0) REVERT: G 333 MET cc_start: 0.6213 (mmp) cc_final: 0.5813 (mmp) REVERT: B 114 VAL cc_start: 0.7032 (m) cc_final: 0.6686 (m) REVERT: C 115 VAL cc_start: 0.6762 (t) cc_final: 0.6468 (m) REVERT: C 178 HIS cc_start: 0.6417 (t-170) cc_final: 0.6137 (t-90) REVERT: C 422 LYS cc_start: 0.8026 (ttmm) cc_final: 0.7713 (ttpp) REVERT: D 115 VAL cc_start: 0.6934 (t) cc_final: 0.6629 (m) REVERT: D 352 LEU cc_start: 0.8324 (mp) cc_final: 0.8018 (mm) outliers start: 39 outliers final: 21 residues processed: 198 average time/residue: 0.4509 time to fit residues: 105.8073 Evaluate side-chains 192 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TRP Chi-restraints excluded: chain A residue 256 THR 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 256 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 469 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 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 265 GLU 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: 0.0060 chunk 11 optimal weight: 7.9990 chunk 164 optimal weight: 0.6980 chunk 134 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 24 optimal weight: 0.0070 chunk 242 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 180 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 overall best weight: 0.4214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4490 r_free = 0.4490 target = 0.202086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.162610 restraints weight = 43267.439| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 3.49 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4068 r_free = 0.4068 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4068 r_free = 0.4068 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20896 Z= 0.111 Angle : 0.550 9.917 28328 Z= 0.276 Chirality : 0.040 0.137 3040 Planarity : 0.004 0.041 3612 Dihedral : 5.731 89.699 3068 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.45 % Allowed : 17.91 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.17), residues: 2476 helix: 1.31 (0.15), residues: 1248 sheet: -1.40 (0.33), residues: 224 loop : -1.29 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 402 TYR 0.024 0.001 TYR C 600 PHE 0.014 0.001 PHE A 179 TRP 0.021 0.001 TRP D 106 HIS 0.004 0.001 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00253 (20896) covalent geometry : angle 0.54964 (28328) hydrogen bonds : bond 0.03490 ( 884) hydrogen bonds : angle 3.78925 ( 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 230 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 TRP cc_start: 0.7572 (OUTLIER) cc_final: 0.7322 (p90) REVERT: G 333 MET cc_start: 0.5212 (mmp) cc_final: 0.4880 (mmp) REVERT: B 114 VAL cc_start: 0.6826 (m) cc_final: 0.6578 (m) outliers start: 31 outliers final: 22 residues processed: 217 average time/residue: 0.4707 time to fit residues: 121.6498 Evaluate side-chains 189 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TRP Chi-restraints excluded: chain A residue 256 THR 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 256 THR Chi-restraints excluded: chain B residue 262 THR 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 209 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 428 MET 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 265 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 218 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 245 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 152 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4459 r_free = 0.4459 target = 0.198647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.158877 restraints weight = 50755.750| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 2.79 r_work: 0.3422 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 20896 Z= 0.203 Angle : 0.636 10.182 28328 Z= 0.322 Chirality : 0.044 0.156 3040 Planarity : 0.004 0.040 3612 Dihedral : 6.146 85.181 3068 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.73 % Allowed : 18.66 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.17), residues: 2476 helix: 1.09 (0.15), residues: 1244 sheet: -1.27 (0.29), residues: 296 loop : -1.40 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 586 TYR 0.028 0.002 TYR A 600 PHE 0.018 0.002 PHE C 179 TRP 0.032 0.002 TRP B 106 HIS 0.006 0.001 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00486 (20896) covalent geometry : angle 0.63591 (28328) hydrogen bonds : bond 0.04293 ( 884) hydrogen bonds : angle 4.06196 ( 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 207 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 170 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 VAL cc_start: 0.7332 (m) cc_final: 0.6970 (m) REVERT: A 182 TRP cc_start: 0.8290 (OUTLIER) cc_final: 0.7898 (p90) REVERT: G 333 MET cc_start: 0.6142 (mmp) cc_final: 0.5885 (mmp) REVERT: D 113 LEU cc_start: 0.6467 (mt) cc_final: 0.6177 (tp) REVERT: D 178 HIS cc_start: 0.6854 (t-170) cc_final: 0.6505 (t-90) outliers start: 37 outliers final: 24 residues processed: 192 average time/residue: 0.5362 time to fit residues: 121.6975 Evaluate side-chains 194 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TRP Chi-restraints excluded: chain A residue 256 THR 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 256 THR 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 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 469 SER Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 265 GLU 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: 2.9990 chunk 226 optimal weight: 0.5980 chunk 74 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 197 optimal weight: 9.9990 chunk 159 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 220 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 HIS ** 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** D 268 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.197399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.156843 restraints weight = 50396.395| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 2.77 r_work: 0.3363 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20896 Z= 0.221 Angle : 0.661 10.124 28328 Z= 0.335 Chirality : 0.045 0.183 3040 Planarity : 0.004 0.040 3612 Dihedral : 6.512 81.356 3068 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.63 % Allowed : 18.98 % 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 aren not related in a simple way. whole: -0.41 (0.17), residues: 2476 helix: 0.95 (0.15), residues: 1240 sheet: -1.27 (0.29), residues: 296 loop : -1.55 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 586 TYR 0.029 0.002 TYR C 600 PHE 0.018 0.002 PHE D 179 TRP 0.035 0.002 TRP D 106 HIS 0.006 0.001 HIS B 478 Details of bonding type rmsd covalent geometry : bond 0.00530 (20896) covalent geometry : angle 0.66137 (28328) hydrogen bonds : bond 0.04418 ( 884) hydrogen bonds : angle 4.16702 ( 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 201 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 LEU cc_start: 0.6534 (mt) cc_final: 0.6247 (tp) REVERT: A 114 VAL cc_start: 0.7259 (m) cc_final: 0.6868 (m) REVERT: A 182 TRP cc_start: 0.8397 (OUTLIER) cc_final: 0.8100 (p90) REVERT: D 113 LEU cc_start: 0.6634 (mt) cc_final: 0.6383 (tp) REVERT: D 178 HIS cc_start: 0.6788 (t-170) cc_final: 0.6480 (t-90) outliers start: 35 outliers final: 23 residues processed: 189 average time/residue: 0.5532 time to fit residues: 122.8721 Evaluate side-chains 183 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 TRP Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 260 GLN 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 256 THR 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 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 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 265 GLU 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.3732 > 50: distance: 59 - 64: 8.675 distance: 64 - 65: 22.782 distance: 65 - 66: 12.065 distance: 65 - 68: 22.427 distance: 66 - 67: 33.992 distance: 66 - 72: 21.953 distance: 68 - 69: 16.120 distance: 69 - 70: 34.246 distance: 70 - 71: 19.217 distance: 72 - 73: 10.594 distance: 72 - 78: 16.814 distance: 73 - 74: 9.909 distance: 73 - 76: 20.510 distance: 74 - 75: 5.583 distance: 74 - 79: 14.754 distance: 76 - 77: 10.132 distance: 77 - 78: 10.737 distance: 79 - 80: 26.406 distance: 80 - 81: 15.877 distance: 80 - 83: 28.641 distance: 81 - 82: 14.291 distance: 81 - 84: 6.510 distance: 84 - 85: 8.334 distance: 85 - 86: 8.754 distance: 85 - 88: 3.864 distance: 86 - 87: 19.015 distance: 86 - 95: 28.648 distance: 88 - 89: 15.189 distance: 89 - 90: 6.095 distance: 90 - 91: 8.791 distance: 92 - 93: 8.882 distance: 92 - 94: 5.874 distance: 96 - 97: 26.345 distance: 96 - 99: 17.758 distance: 97 - 98: 11.454 distance: 97 - 102: 44.829 distance: 99 - 100: 8.205 distance: 99 - 101: 7.506 distance: 102 - 103: 19.057 distance: 103 - 104: 12.619 distance: 103 - 106: 16.105 distance: 104 - 105: 13.787 distance: 104 - 110: 22.753 distance: 106 - 107: 13.561 distance: 107 - 108: 3.423 distance: 107 - 109: 8.676 distance: 110 - 111: 20.872 distance: 111 - 112: 18.104 distance: 111 - 114: 7.675 distance: 112 - 113: 12.614 distance: 113 - 188: 33.408 distance: 114 - 115: 25.183 distance: 115 - 116: 13.528 distance: 115 - 117: 10.826 distance: 118 - 119: 24.300 distance: 119 - 120: 25.472 distance: 119 - 122: 10.337 distance: 120 - 121: 34.991 distance: 120 - 129: 34.276 distance: 122 - 123: 21.718 distance: 123 - 124: 19.035 distance: 124 - 126: 18.780 distance: 125 - 127: 14.037 distance: 126 - 128: 5.725 distance: 127 - 128: 9.223 distance: 129 - 130: 53.115 distance: 130 - 131: 38.377 distance: 130 - 133: 34.656 distance: 131 - 132: 19.375 distance: 131 - 137: 12.315 distance: 133 - 134: 50.665 distance: 134 - 135: 12.419 distance: 134 - 136: 34.784 distance: 137 - 138: 8.091 distance: 138 - 139: 23.660 distance: 138 - 141: 26.841 distance: 139 - 140: 22.061 distance: 139 - 144: 15.416 distance: 140 - 165: 32.468 distance: 141 - 142: 36.048 distance: 141 - 143: 24.214