Starting phenix.real_space_refine on Wed Mar 4 15:11:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vxn_21445/03_2026/6vxn_21445.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vxn_21445/03_2026/6vxn_21445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vxn_21445/03_2026/6vxn_21445.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vxn_21445/03_2026/6vxn_21445.map" model { file = "/net/cci-nas-00/data/ceres_data/6vxn_21445/03_2026/6vxn_21445.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vxn_21445/03_2026/6vxn_21445.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 77 5.16 5 C 9296 2.51 5 N 2394 2.21 5 O 2618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14385 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2043 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain breaks: 3 Chain: "B" Number of atoms: 2043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2043 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain breaks: 3 Chain: "C" Number of atoms: 2043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2043 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain breaks: 3 Chain: "D" Number of atoms: 2043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2043 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain breaks: 3 Chain: "E" Number of atoms: 2043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2043 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain breaks: 3 Chain: "F" Number of atoms: 2043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2043 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain breaks: 3 Chain: "G" Number of atoms: 2043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2043 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain breaks: 3 Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'D12': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'D12': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'D12': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'D12': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'D12': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.07, per 1000 atoms: 0.21 Number of scatterers: 14385 At special positions: 0 Unit cell: (121, 119.9, 101.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 77 16.00 O 2618 8.00 N 2394 7.00 C 9296 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: 1.35 Conformation dependent library (CDL) restraints added in 556.9 milliseconds 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3458 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 8 sheets defined 56.4% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 204 through 227 Proline residue: A 212 - end of helix removed outlier: 3.760A pdb=" N ILE A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 267 Processing helix chain 'A' and resid 277 through 300 Processing helix chain 'A' and resid 315 through 341 removed outlier: 4.508A pdb=" N VAL A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 385 removed outlier: 3.665A pdb=" N SER A 385 " --> pdb=" O SER A 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 382 through 385' Processing helix chain 'A' and resid 410 through 412 No H-bonds generated for 'chain 'A' and resid 410 through 412' Processing helix chain 'A' and resid 413 through 428 removed outlier: 3.514A pdb=" N ASN A 428 " --> pdb=" O MET A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 484 removed outlier: 3.837A pdb=" N TYR A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS A 484 " --> pdb=" O ILE A 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 227 Proline residue: B 212 - end of helix removed outlier: 3.761A pdb=" N ILE B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 267 Processing helix chain 'B' and resid 277 through 300 Processing helix chain 'B' and resid 315 through 341 removed outlier: 4.508A pdb=" N VAL B 319 " --> pdb=" O GLY B 315 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 385 removed outlier: 3.664A pdb=" N SER B 385 " --> pdb=" O SER B 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 382 through 385' Processing helix chain 'B' and resid 410 through 412 No H-bonds generated for 'chain 'B' and resid 410 through 412' Processing helix chain 'B' and resid 413 through 428 removed outlier: 3.514A pdb=" N ASN B 428 " --> pdb=" O MET B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 484 removed outlier: 3.837A pdb=" N TYR B 467 " --> pdb=" O LYS B 463 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS B 484 " --> pdb=" O ILE B 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 227 Proline residue: C 212 - end of helix removed outlier: 3.760A pdb=" N ILE C 225 " --> pdb=" O ALA C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 267 Processing helix chain 'C' and resid 277 through 300 Processing helix chain 'C' and resid 315 through 341 removed outlier: 4.508A pdb=" N VAL C 319 " --> pdb=" O GLY C 315 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN C 339 " --> pdb=" O GLY C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 385 removed outlier: 3.665A pdb=" N SER C 385 " --> pdb=" O SER C 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 382 through 385' Processing helix chain 'C' and resid 410 through 412 No H-bonds generated for 'chain 'C' and resid 410 through 412' Processing helix chain 'C' and resid 413 through 428 removed outlier: 3.514A pdb=" N ASN C 428 " --> pdb=" O MET C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 484 removed outlier: 3.837A pdb=" N TYR C 467 " --> pdb=" O LYS C 463 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS C 484 " --> pdb=" O ILE C 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 227 Proline residue: D 212 - end of helix removed outlier: 3.760A pdb=" N ILE D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 267 Processing helix chain 'D' and resid 277 through 300 Processing helix chain 'D' and resid 315 through 341 removed outlier: 4.508A pdb=" N VAL D 319 " --> pdb=" O GLY D 315 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN D 339 " --> pdb=" O GLY D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 385 removed outlier: 3.665A pdb=" N SER D 385 " --> pdb=" O SER D 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 382 through 385' Processing helix chain 'D' and resid 410 through 412 No H-bonds generated for 'chain 'D' and resid 410 through 412' Processing helix chain 'D' and resid 413 through 428 removed outlier: 3.514A pdb=" N ASN D 428 " --> pdb=" O MET D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 484 removed outlier: 3.837A pdb=" N TYR D 467 " --> pdb=" O LYS D 463 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS D 484 " --> pdb=" O ILE D 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 227 Proline residue: E 212 - end of helix removed outlier: 3.760A pdb=" N ILE E 225 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 267 Processing helix chain 'E' and resid 277 through 300 Processing helix chain 'E' and resid 315 through 341 removed outlier: 4.507A pdb=" N VAL E 319 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN E 339 " --> pdb=" O GLY E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 385 removed outlier: 3.665A pdb=" N SER E 385 " --> pdb=" O SER E 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 382 through 385' Processing helix chain 'E' and resid 410 through 412 No H-bonds generated for 'chain 'E' and resid 410 through 412' Processing helix chain 'E' and resid 413 through 428 removed outlier: 3.514A pdb=" N ASN E 428 " --> pdb=" O MET E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 484 removed outlier: 3.837A pdb=" N TYR E 467 " --> pdb=" O LYS E 463 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS E 484 " --> pdb=" O ILE E 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 227 Proline residue: F 212 - end of helix removed outlier: 3.760A pdb=" N ILE F 225 " --> pdb=" O ALA F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 267 Processing helix chain 'F' and resid 277 through 300 Processing helix chain 'F' and resid 315 through 341 removed outlier: 4.508A pdb=" N VAL F 319 " --> pdb=" O GLY F 315 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN F 339 " --> pdb=" O GLY F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 385 removed outlier: 3.665A pdb=" N SER F 385 " --> pdb=" O SER F 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 382 through 385' Processing helix chain 'F' and resid 410 through 412 No H-bonds generated for 'chain 'F' and resid 410 through 412' Processing helix chain 'F' and resid 413 through 428 removed outlier: 3.514A pdb=" N ASN F 428 " --> pdb=" O MET F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 484 removed outlier: 3.838A pdb=" N TYR F 467 " --> pdb=" O LYS F 463 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS F 484 " --> pdb=" O ILE F 480 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 227 Proline residue: G 212 - end of helix removed outlier: 3.760A pdb=" N ILE G 225 " --> pdb=" O ALA G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 267 Processing helix chain 'G' and resid 277 through 300 Processing helix chain 'G' and resid 315 through 341 removed outlier: 4.508A pdb=" N VAL G 319 " --> pdb=" O GLY G 315 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN G 339 " --> pdb=" O GLY G 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 382 through 385 removed outlier: 3.664A pdb=" N SER G 385 " --> pdb=" O SER G 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 382 through 385' Processing helix chain 'G' and resid 410 through 412 No H-bonds generated for 'chain 'G' and resid 410 through 412' Processing helix chain 'G' and resid 413 through 428 removed outlier: 3.513A pdb=" N ASN G 428 " --> pdb=" O MET G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 484 removed outlier: 3.837A pdb=" N TYR G 467 " --> pdb=" O LYS G 463 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS G 484 " --> pdb=" O ILE G 480 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 349 through 352 removed outlier: 3.533A pdb=" N VAL A 355 " --> pdb=" O ALA A 352 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL A 359 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU A 370 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE G 389 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL G 355 " --> pdb=" O ALA G 352 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL G 359 " --> pdb=" O LEU G 370 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU G 370 " --> pdb=" O VAL G 359 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL F 355 " --> pdb=" O ALA F 352 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL F 359 " --> pdb=" O LEU F 370 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU F 370 " --> pdb=" O VAL F 359 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE E 389 " --> pdb=" O LEU F 378 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL E 355 " --> pdb=" O ALA E 352 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL E 359 " --> pdb=" O LEU E 370 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU E 370 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL D 355 " --> pdb=" O ALA D 352 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL D 359 " --> pdb=" O LEU D 370 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU D 370 " --> pdb=" O VAL D 359 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 355 " --> pdb=" O ALA C 352 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N VAL C 359 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU C 370 " --> pdb=" O VAL C 359 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 355 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL B 359 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 370 " --> pdb=" O VAL B 359 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 439 through 446 removed outlier: 6.967A pdb=" N GLU A 451 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL A 445 " --> pdb=" O PHE A 449 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N PHE A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER A 487 " --> pdb=" O GLN A 407 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 439 through 446 removed outlier: 6.968A pdb=" N GLU B 451 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL B 445 " --> pdb=" O PHE B 449 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N PHE B 449 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER B 487 " --> pdb=" O GLN B 407 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 439 through 446 removed outlier: 6.967A pdb=" N GLU C 451 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL C 445 " --> pdb=" O PHE C 449 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N PHE C 449 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER C 487 " --> pdb=" O GLN C 407 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 439 through 446 removed outlier: 6.967A pdb=" N GLU D 451 " --> pdb=" O SER D 443 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL D 445 " --> pdb=" O PHE D 449 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N PHE D 449 " --> pdb=" O VAL D 445 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER D 487 " --> pdb=" O GLN D 407 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 439 through 446 removed outlier: 6.967A pdb=" N GLU E 451 " --> pdb=" O SER E 443 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL E 445 " --> pdb=" O PHE E 449 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N PHE E 449 " --> pdb=" O VAL E 445 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER E 487 " --> pdb=" O GLN E 407 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 439 through 446 removed outlier: 6.966A pdb=" N GLU F 451 " --> pdb=" O SER F 443 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N VAL F 445 " --> pdb=" O PHE F 449 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N PHE F 449 " --> pdb=" O VAL F 445 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER F 487 " --> pdb=" O GLN F 407 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 439 through 446 removed outlier: 6.967A pdb=" N GLU G 451 " --> pdb=" O SER G 443 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL G 445 " --> pdb=" O PHE G 449 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N PHE G 449 " --> pdb=" O VAL G 445 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER G 487 " --> pdb=" O GLN G 407 " (cutoff:3.500A) 979 hydrogen bonds defined for protein. 2901 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.07 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4413 1.34 - 1.46: 3168 1.46 - 1.58: 6881 1.58 - 1.70: 0 1.70 - 1.82: 140 Bond restraints: 14602 Sorted by residual: bond pdb=" C PRO C 343 " pdb=" N PHE C 344 " ideal model delta sigma weight residual 1.330 1.462 -0.132 1.26e-02 6.30e+03 1.10e+02 bond pdb=" C PRO D 343 " pdb=" N PHE D 344 " ideal model delta sigma weight residual 1.330 1.462 -0.132 1.26e-02 6.30e+03 1.10e+02 bond pdb=" C PRO A 343 " pdb=" N PHE A 344 " ideal model delta sigma weight residual 1.330 1.462 -0.132 1.26e-02 6.30e+03 1.09e+02 bond pdb=" C PRO F 343 " pdb=" N PHE F 344 " ideal model delta sigma weight residual 1.330 1.462 -0.131 1.26e-02 6.30e+03 1.09e+02 bond pdb=" C PRO G 343 " pdb=" N PHE G 344 " ideal model delta sigma weight residual 1.330 1.461 -0.131 1.26e-02 6.30e+03 1.08e+02 ... (remaining 14597 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 18786 2.14 - 4.28: 695 4.28 - 6.42: 120 6.42 - 8.56: 55 8.56 - 10.69: 28 Bond angle restraints: 19684 Sorted by residual: angle pdb=" C MET E 413 " pdb=" N ILE E 414 " pdb=" CA ILE E 414 " ideal model delta sigma weight residual 120.24 124.10 -3.86 6.30e-01 2.52e+00 3.75e+01 angle pdb=" C MET B 413 " pdb=" N ILE B 414 " pdb=" CA ILE B 414 " ideal model delta sigma weight residual 120.24 124.09 -3.85 6.30e-01 2.52e+00 3.74e+01 angle pdb=" C MET G 413 " pdb=" N ILE G 414 " pdb=" CA ILE G 414 " ideal model delta sigma weight residual 120.24 124.08 -3.84 6.30e-01 2.52e+00 3.71e+01 angle pdb=" C MET C 413 " pdb=" N ILE C 414 " pdb=" CA ILE C 414 " ideal model delta sigma weight residual 120.24 124.07 -3.83 6.30e-01 2.52e+00 3.70e+01 angle pdb=" C MET A 413 " pdb=" N ILE A 414 " pdb=" CA ILE A 414 " ideal model delta sigma weight residual 120.24 124.06 -3.82 6.30e-01 2.52e+00 3.67e+01 ... (remaining 19679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.82: 7601 14.82 - 29.65: 757 29.65 - 44.47: 280 44.47 - 59.29: 126 59.29 - 74.11: 42 Dihedral angle restraints: 8806 sinusoidal: 3479 harmonic: 5327 Sorted by residual: dihedral pdb=" CA MET C 297 " pdb=" C MET C 297 " pdb=" N ALA C 298 " pdb=" CA ALA C 298 " ideal model delta harmonic sigma weight residual 180.00 164.03 15.97 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA MET F 297 " pdb=" C MET F 297 " pdb=" N ALA F 298 " pdb=" CA ALA F 298 " ideal model delta harmonic sigma weight residual 180.00 164.04 15.96 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA MET B 297 " pdb=" C MET B 297 " pdb=" N ALA B 298 " pdb=" CA ALA B 298 " ideal model delta harmonic sigma weight residual 180.00 164.05 15.95 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 8803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1958 0.074 - 0.147: 332 0.147 - 0.221: 48 0.221 - 0.294: 0 0.294 - 0.368: 7 Chirality restraints: 2345 Sorted by residual: chirality pdb=" CB ILE D 263 " pdb=" CA ILE D 263 " pdb=" CG1 ILE D 263 " pdb=" CG2 ILE D 263 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CB ILE B 263 " pdb=" CA ILE B 263 " pdb=" CG1 ILE B 263 " pdb=" CG2 ILE B 263 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CB ILE A 263 " pdb=" CA ILE A 263 " pdb=" CG1 ILE A 263 " pdb=" CG2 ILE A 263 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.36e+00 ... (remaining 2342 not shown) Planarity restraints: 2429 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 421 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.64e+00 pdb=" C ILE D 421 " -0.041 2.00e-02 2.50e+03 pdb=" O ILE D 421 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS D 422 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 421 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C ILE B 421 " 0.041 2.00e-02 2.50e+03 pdb=" O ILE B 421 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS B 422 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 421 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.49e+00 pdb=" C ILE C 421 " 0.041 2.00e-02 2.50e+03 pdb=" O ILE C 421 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS C 422 " -0.014 2.00e-02 2.50e+03 ... (remaining 2426 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 4494 2.85 - 3.36: 12935 3.36 - 3.87: 22710 3.87 - 4.39: 25347 4.39 - 4.90: 44631 Nonbonded interactions: 110117 Sorted by model distance: nonbonded pdb=" O GLU D 465 " pdb=" OG1 THR D 469 " model vdw 2.332 3.040 nonbonded pdb=" O GLU A 465 " pdb=" OG1 THR A 469 " model vdw 2.333 3.040 nonbonded pdb=" O GLU F 465 " pdb=" OG1 THR F 469 " model vdw 2.333 3.040 nonbonded pdb=" O GLU G 465 " pdb=" OG1 THR G 469 " model vdw 2.333 3.040 nonbonded pdb=" O GLU E 465 " pdb=" OG1 THR E 469 " model vdw 2.333 3.040 ... (remaining 110112 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.380 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 : 0.013 0.149 14602 Z= 0.658 Angle : 1.068 10.694 19684 Z= 0.572 Chirality : 0.062 0.368 2345 Planarity : 0.007 0.042 2429 Dihedral : 15.677 74.113 5348 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.00 % Allowed : 13.00 % Favored : 87.00 % 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 are not related in a simple way. whole: -3.41 (0.16), residues: 1806 helix: -1.92 (0.13), residues: 1015 sheet: -2.20 (0.23), residues: 364 loop : -2.41 (0.23), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 444 TYR 0.012 0.002 TYR F 441 PHE 0.017 0.002 PHE E 384 TRP 0.022 0.003 TRP G 206 HIS 0.003 0.001 HIS C 439 Details of bonding type rmsd covalent geometry : bond 0.01289 (14602) covalent geometry : angle 1.06760 (19684) hydrogen bonds : bond 0.12784 ( 979) hydrogen bonds : angle 6.27726 ( 2901) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 TRP cc_start: 0.0446 (m100) cc_final: -0.0181 (m-90) REVERT: A 258 TRP cc_start: 0.8423 (t60) cc_final: 0.8146 (t60) REVERT: A 292 PHE cc_start: 0.7860 (t80) cc_final: 0.7403 (t80) REVERT: B 228 MET cc_start: 0.6865 (tpp) cc_final: 0.6629 (mmp) REVERT: B 292 PHE cc_start: 0.7815 (t80) cc_final: 0.7494 (t80) REVERT: B 323 PHE cc_start: 0.8960 (m-10) cc_final: 0.8741 (m-80) REVERT: C 258 TRP cc_start: 0.7993 (t60) cc_final: 0.7742 (t60) REVERT: C 261 ASN cc_start: 0.8834 (m110) cc_final: 0.8552 (m110) REVERT: C 292 PHE cc_start: 0.7909 (t80) cc_final: 0.7705 (t80) REVERT: C 339 GLN cc_start: 0.8921 (mm-40) cc_final: 0.8469 (mm-40) REVERT: D 214 ARG cc_start: 0.5990 (ptt90) cc_final: 0.5441 (ptm-80) REVERT: D 224 GLN cc_start: 0.7509 (tt0) cc_final: 0.7235 (tp-100) REVERT: D 323 PHE cc_start: 0.8834 (m-10) cc_final: 0.8158 (m-80) REVERT: E 339 GLN cc_start: 0.8891 (mm-40) cc_final: 0.8454 (mm-40) REVERT: F 292 PHE cc_start: 0.8070 (t80) cc_final: 0.7856 (t80) REVERT: G 258 TRP cc_start: 0.8106 (t60) cc_final: 0.7888 (t60) REVERT: G 292 PHE cc_start: 0.7939 (t80) cc_final: 0.7519 (OUTLIER) outliers start: 0 outliers final: 5 residues processed: 310 average time/residue: 0.7190 time to fit residues: 240.5220 Evaluate side-chains 192 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 188 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain E residue 410 ASP Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 410 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 ASN B 407 GLN B 457 ASN C 381 ASN C 416 GLN C 457 ASN D 457 ASN E 457 ASN F 457 ASN G 407 GLN G 457 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.116648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.074394 restraints weight = 27489.996| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.96 r_work: 0.2906 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14602 Z= 0.137 Angle : 0.648 8.557 19684 Z= 0.321 Chirality : 0.043 0.223 2345 Planarity : 0.005 0.040 2429 Dihedral : 7.971 119.191 2017 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.67 % Allowed : 21.91 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.19), residues: 1806 helix: 0.28 (0.16), residues: 1008 sheet: -1.61 (0.25), residues: 350 loop : -1.73 (0.24), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 342 TYR 0.017 0.001 TYR F 256 PHE 0.017 0.001 PHE F 323 TRP 0.010 0.001 TRP F 206 HIS 0.001 0.000 HIS D 439 Details of bonding type rmsd covalent geometry : bond 0.00285 (14602) covalent geometry : angle 0.64765 (19684) hydrogen bonds : bond 0.04116 ( 979) hydrogen bonds : angle 4.39025 ( 2901) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 216 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 TRP cc_start: -0.0367 (m100) cc_final: -0.0704 (p90) REVERT: A 266 MET cc_start: 0.6869 (ppp) cc_final: 0.6587 (mmt) REVERT: A 413 MET cc_start: 0.8192 (mmm) cc_final: 0.7960 (mmm) REVERT: B 228 MET cc_start: 0.6648 (tpp) cc_final: 0.6368 (mmp) REVERT: B 323 PHE cc_start: 0.8921 (m-10) cc_final: 0.8668 (m-80) REVERT: B 348 ASP cc_start: 0.8750 (m-30) cc_final: 0.8547 (m-30) REVERT: B 424 MET cc_start: 0.9019 (tmm) cc_final: 0.8658 (tmm) REVERT: D 228 MET cc_start: 0.4877 (mmp) cc_final: 0.4355 (mmp) REVERT: D 266 MET cc_start: 0.7400 (tmm) cc_final: 0.6999 (ttt) REVERT: D 319 VAL cc_start: 0.8709 (t) cc_final: 0.8304 (m) REVERT: D 323 PHE cc_start: 0.8908 (m-10) cc_final: 0.8492 (m-80) REVERT: D 410 ASP cc_start: 0.8599 (t0) cc_final: 0.8372 (t0) REVERT: D 413 MET cc_start: 0.7961 (mmm) cc_final: 0.7759 (mmm) REVERT: E 224 GLN cc_start: 0.7375 (tp-100) cc_final: 0.7105 (tt0) REVERT: E 339 GLN cc_start: 0.9228 (mm-40) cc_final: 0.8853 (mm-40) REVERT: E 348 ASP cc_start: 0.8516 (m-30) cc_final: 0.8240 (m-30) REVERT: F 292 PHE cc_start: 0.7947 (t80) cc_final: 0.7709 (t80) REVERT: F 410 ASP cc_start: 0.8640 (t0) cc_final: 0.8261 (t0) REVERT: F 482 LYS cc_start: 0.9395 (OUTLIER) cc_final: 0.9149 (mttm) REVERT: G 266 MET cc_start: 0.6998 (ppp) cc_final: 0.6347 (mmt) REVERT: G 292 PHE cc_start: 0.7885 (t80) cc_final: 0.7539 (t80) REVERT: G 410 ASP cc_start: 0.8564 (t0) cc_final: 0.8262 (t0) REVERT: G 413 MET cc_start: 0.8539 (mmm) cc_final: 0.8281 (mmm) REVERT: G 416 GLN cc_start: 0.8053 (mp10) cc_final: 0.7784 (mp10) outliers start: 26 outliers final: 7 residues processed: 228 average time/residue: 0.5451 time to fit residues: 137.6739 Evaluate side-chains 195 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 187 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain F residue 387 GLN Chi-restraints excluded: chain F residue 482 LYS Chi-restraints excluded: chain G residue 215 TYR Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 319 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 136 optimal weight: 20.0000 chunk 1 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 176 optimal weight: 0.0010 chunk 137 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 ASN C 339 GLN C 407 GLN C 416 GLN E 407 GLN G 358 GLN G 407 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.115918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.074184 restraints weight = 27513.858| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.92 r_work: 0.2904 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14602 Z= 0.124 Angle : 0.608 8.939 19684 Z= 0.298 Chirality : 0.042 0.235 2345 Planarity : 0.004 0.032 2429 Dihedral : 6.300 53.033 2009 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.79 % Allowed : 23.32 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.20), residues: 1806 helix: 1.16 (0.17), residues: 1008 sheet: -1.41 (0.26), residues: 350 loop : -1.33 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 326 TYR 0.015 0.001 TYR C 256 PHE 0.016 0.001 PHE G 254 TRP 0.008 0.001 TRP F 206 HIS 0.002 0.000 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00261 (14602) covalent geometry : angle 0.60799 (19684) hydrogen bonds : bond 0.03602 ( 979) hydrogen bonds : angle 4.02108 ( 2901) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 TRP cc_start: -0.0135 (m100) cc_final: -0.0675 (p90) REVERT: A 266 MET cc_start: 0.6959 (ppp) cc_final: 0.6635 (mmt) REVERT: A 348 ASP cc_start: 0.8847 (m-30) cc_final: 0.8586 (m-30) REVERT: B 348 ASP cc_start: 0.8729 (m-30) cc_final: 0.8526 (m-30) REVERT: B 424 MET cc_start: 0.9052 (tmm) cc_final: 0.8665 (tmm) REVERT: C 278 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8052 (tm-30) REVERT: C 468 ASN cc_start: 0.8756 (m-40) cc_final: 0.8388 (m-40) REVERT: D 228 MET cc_start: 0.4959 (mmp) cc_final: 0.4616 (mmp) REVERT: D 266 MET cc_start: 0.7341 (tmm) cc_final: 0.6906 (ttt) REVERT: D 319 VAL cc_start: 0.8668 (t) cc_final: 0.8289 (m) REVERT: D 323 PHE cc_start: 0.8901 (m-10) cc_final: 0.8487 (m-80) REVERT: D 348 ASP cc_start: 0.8589 (m-30) cc_final: 0.8298 (m-30) REVERT: D 410 ASP cc_start: 0.8466 (t0) cc_final: 0.8177 (t0) REVERT: E 278 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8268 (pp20) REVERT: E 348 ASP cc_start: 0.8586 (m-30) cc_final: 0.8272 (m-30) REVERT: E 362 MET cc_start: 0.9357 (OUTLIER) cc_final: 0.9120 (mtm) REVERT: F 292 PHE cc_start: 0.7953 (t80) cc_final: 0.7704 (t80) REVERT: F 482 LYS cc_start: 0.9379 (OUTLIER) cc_final: 0.9147 (mttm) REVERT: G 266 MET cc_start: 0.6799 (ppp) cc_final: 0.6254 (mmt) REVERT: G 292 PHE cc_start: 0.7880 (t80) cc_final: 0.7511 (t80) REVERT: G 410 ASP cc_start: 0.8572 (t0) cc_final: 0.8282 (t0) REVERT: G 416 GLN cc_start: 0.8059 (mp10) cc_final: 0.7793 (mp10) outliers start: 28 outliers final: 9 residues processed: 208 average time/residue: 0.5656 time to fit residues: 129.5381 Evaluate side-chains 194 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 482 LYS Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 346 MET Chi-restraints excluded: chain G residue 407 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 140 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 25 optimal weight: 0.0670 chunk 90 optimal weight: 0.0020 chunk 86 optimal weight: 0.0040 chunk 126 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 101 optimal weight: 0.1980 overall best weight: 0.2538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 407 GLN A 470 GLN B 339 GLN B 470 GLN C 407 GLN C 416 GLN C 470 GLN D 381 ASN E 339 GLN E 470 GLN F 470 GLN G 358 GLN G 470 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.116653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.075051 restraints weight = 27725.871| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.90 r_work: 0.2934 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14602 Z= 0.112 Angle : 0.597 10.174 19684 Z= 0.289 Chirality : 0.041 0.215 2345 Planarity : 0.003 0.030 2429 Dihedral : 5.720 49.130 2009 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.99 % Allowed : 24.98 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.20), residues: 1806 helix: 1.49 (0.17), residues: 1001 sheet: -1.28 (0.27), residues: 350 loop : -1.08 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 326 TYR 0.012 0.001 TYR E 256 PHE 0.018 0.001 PHE G 254 TRP 0.011 0.001 TRP A 258 HIS 0.001 0.000 HIS E 439 Details of bonding type rmsd covalent geometry : bond 0.00226 (14602) covalent geometry : angle 0.59685 (19684) hydrogen bonds : bond 0.03206 ( 979) hydrogen bonds : angle 3.81292 ( 2901) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 TRP cc_start: -0.0522 (m100) cc_final: -0.0963 (p90) REVERT: A 266 MET cc_start: 0.6988 (ppp) cc_final: 0.6744 (mmt) REVERT: A 348 ASP cc_start: 0.8782 (m-30) cc_final: 0.8533 (m-30) REVERT: A 413 MET cc_start: 0.8343 (mmm) cc_final: 0.8124 (mmm) REVERT: A 424 MET cc_start: 0.8848 (tmm) cc_final: 0.8560 (OUTLIER) REVERT: B 319 VAL cc_start: 0.8615 (m) cc_final: 0.8278 (m) REVERT: B 323 PHE cc_start: 0.8882 (m-10) cc_final: 0.8621 (m-80) REVERT: B 348 ASP cc_start: 0.8661 (m-30) cc_final: 0.8032 (m-30) REVERT: B 424 MET cc_start: 0.8995 (tmm) cc_final: 0.8603 (tmm) REVERT: C 278 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8001 (tm-30) REVERT: D 228 MET cc_start: 0.5190 (mmp) cc_final: 0.4938 (mmp) REVERT: D 266 MET cc_start: 0.7319 (tmm) cc_final: 0.6901 (ttt) REVERT: D 319 VAL cc_start: 0.8664 (t) cc_final: 0.8308 (m) REVERT: D 323 PHE cc_start: 0.8855 (m-10) cc_final: 0.8443 (m-80) REVERT: D 348 ASP cc_start: 0.8557 (m-30) cc_final: 0.8260 (m-30) REVERT: D 410 ASP cc_start: 0.8463 (t0) cc_final: 0.8158 (t0) REVERT: E 224 GLN cc_start: 0.7476 (tp-100) cc_final: 0.7153 (tt0) REVERT: E 348 ASP cc_start: 0.8557 (m-30) cc_final: 0.8258 (m-30) REVERT: E 362 MET cc_start: 0.9383 (OUTLIER) cc_final: 0.9139 (mtm) REVERT: E 413 MET cc_start: 0.8436 (mmp) cc_final: 0.7923 (mmp) REVERT: F 292 PHE cc_start: 0.7898 (t80) cc_final: 0.7644 (t80) REVERT: G 266 MET cc_start: 0.6902 (ppp) cc_final: 0.6405 (mmt) REVERT: G 292 PHE cc_start: 0.7853 (t80) cc_final: 0.7494 (t80) REVERT: G 410 ASP cc_start: 0.8484 (t0) cc_final: 0.8228 (t0) REVERT: G 416 GLN cc_start: 0.8104 (mp10) cc_final: 0.7787 (mp10) outliers start: 31 outliers final: 9 residues processed: 210 average time/residue: 0.5896 time to fit residues: 136.0751 Evaluate side-chains 190 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 319 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 120 optimal weight: 4.9990 chunk 104 optimal weight: 20.0000 chunk 75 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 171 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 144 optimal weight: 0.0270 chunk 32 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 407 GLN C 339 GLN G 358 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.116207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.074715 restraints weight = 27614.241| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.86 r_work: 0.2914 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14602 Z= 0.119 Angle : 0.600 9.459 19684 Z= 0.293 Chirality : 0.041 0.246 2345 Planarity : 0.003 0.028 2429 Dihedral : 5.413 43.298 2009 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.54 % Allowed : 26.14 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.20), residues: 1806 helix: 1.67 (0.17), residues: 1001 sheet: -1.14 (0.28), residues: 350 loop : -0.89 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 326 TYR 0.017 0.001 TYR C 256 PHE 0.018 0.001 PHE G 254 TRP 0.009 0.001 TRP A 258 HIS 0.001 0.000 HIS B 439 Details of bonding type rmsd covalent geometry : bond 0.00254 (14602) covalent geometry : angle 0.59994 (19684) hydrogen bonds : bond 0.03209 ( 979) hydrogen bonds : angle 3.75536 ( 2901) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 206 TRP cc_start: -0.0720 (m100) cc_final: -0.1334 (p90) REVERT: A 266 MET cc_start: 0.6980 (ppp) cc_final: 0.6716 (mmt) REVERT: A 348 ASP cc_start: 0.8818 (m-30) cc_final: 0.8575 (m-30) REVERT: A 413 MET cc_start: 0.8420 (mmm) cc_final: 0.8173 (mmm) REVERT: A 416 GLN cc_start: 0.7743 (mp10) cc_final: 0.7528 (mp10) REVERT: A 424 MET cc_start: 0.8863 (tmm) cc_final: 0.8628 (OUTLIER) REVERT: B 348 ASP cc_start: 0.8706 (m-30) cc_final: 0.8096 (m-30) REVERT: B 424 MET cc_start: 0.8987 (tmm) cc_final: 0.8646 (tmm) REVERT: C 410 ASP cc_start: 0.8426 (t0) cc_final: 0.8203 (t0) REVERT: D 228 MET cc_start: 0.5087 (mmp) cc_final: 0.4853 (mmp) REVERT: D 266 MET cc_start: 0.7284 (tmm) cc_final: 0.6875 (ttt) REVERT: D 319 VAL cc_start: 0.8684 (t) cc_final: 0.8298 (m) REVERT: D 323 PHE cc_start: 0.8864 (m-10) cc_final: 0.8444 (m-80) REVERT: D 348 ASP cc_start: 0.8593 (m-30) cc_final: 0.8273 (m-30) REVERT: D 410 ASP cc_start: 0.8475 (t0) cc_final: 0.8183 (t0) REVERT: E 224 GLN cc_start: 0.7368 (tp-100) cc_final: 0.7005 (tt0) REVERT: E 348 ASP cc_start: 0.8631 (m-30) cc_final: 0.8335 (m-30) REVERT: E 362 MET cc_start: 0.9400 (OUTLIER) cc_final: 0.9161 (mtm) REVERT: E 413 MET cc_start: 0.8529 (mmp) cc_final: 0.8233 (mmp) REVERT: F 292 PHE cc_start: 0.7904 (t80) cc_final: 0.7637 (t80) REVERT: G 266 MET cc_start: 0.6827 (ppp) cc_final: 0.6358 (mmt) REVERT: G 292 PHE cc_start: 0.8007 (t80) cc_final: 0.7628 (t80) REVERT: G 410 ASP cc_start: 0.8423 (t0) cc_final: 0.8180 (t0) REVERT: G 416 GLN cc_start: 0.8129 (mp10) cc_final: 0.7732 (mp10) outliers start: 24 outliers final: 9 residues processed: 202 average time/residue: 0.5688 time to fit residues: 126.7050 Evaluate side-chains 189 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 180 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 346 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 123 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 100 optimal weight: 0.4980 chunk 98 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 178 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN B 407 GLN B 416 GLN G 358 GLN G 407 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.113192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.071616 restraints weight = 27604.531| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.85 r_work: 0.2850 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14602 Z= 0.163 Angle : 0.640 10.004 19684 Z= 0.313 Chirality : 0.043 0.229 2345 Planarity : 0.003 0.028 2429 Dihedral : 5.512 42.069 2009 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.92 % Allowed : 25.88 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.20), residues: 1806 helix: 1.75 (0.17), residues: 1008 sheet: -0.72 (0.30), residues: 315 loop : -0.87 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 326 TYR 0.017 0.001 TYR E 256 PHE 0.020 0.001 PHE G 254 TRP 0.013 0.001 TRP A 258 HIS 0.002 0.001 HIS B 439 Details of bonding type rmsd covalent geometry : bond 0.00368 (14602) covalent geometry : angle 0.63996 (19684) hydrogen bonds : bond 0.03573 ( 979) hydrogen bonds : angle 3.87911 ( 2901) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 0.548 Fit side-chains REVERT: A 206 TRP cc_start: -0.0582 (m100) cc_final: -0.1336 (p90) REVERT: A 266 MET cc_start: 0.6802 (ppp) cc_final: 0.6512 (mmt) REVERT: A 348 ASP cc_start: 0.8865 (m-30) cc_final: 0.8402 (m-30) REVERT: B 323 PHE cc_start: 0.8903 (m-10) cc_final: 0.8609 (m-80) REVERT: B 416 GLN cc_start: 0.8409 (pt0) cc_final: 0.8143 (pm20) REVERT: B 424 MET cc_start: 0.8967 (tmm) cc_final: 0.8619 (OUTLIER) REVERT: C 348 ASP cc_start: 0.8943 (m-30) cc_final: 0.8738 (m-30) REVERT: C 408 ILE cc_start: 0.8788 (tp) cc_final: 0.8550 (tt) REVERT: C 410 ASP cc_start: 0.8345 (t0) cc_final: 0.8067 (t0) REVERT: D 228 MET cc_start: 0.5112 (mmp) cc_final: 0.4895 (mmp) REVERT: D 266 MET cc_start: 0.7357 (tmm) cc_final: 0.6958 (ttt) REVERT: D 319 VAL cc_start: 0.8567 (t) cc_final: 0.8137 (m) REVERT: D 323 PHE cc_start: 0.8876 (m-10) cc_final: 0.8458 (m-80) REVERT: D 348 ASP cc_start: 0.8765 (m-30) cc_final: 0.8500 (m-30) REVERT: D 410 ASP cc_start: 0.8480 (t0) cc_final: 0.8150 (t0) REVERT: E 261 ASN cc_start: 0.8091 (m110) cc_final: 0.7623 (m110) REVERT: E 348 ASP cc_start: 0.8756 (m-30) cc_final: 0.8508 (m-30) REVERT: E 362 MET cc_start: 0.9419 (OUTLIER) cc_final: 0.9197 (mtm) REVERT: E 413 MET cc_start: 0.8529 (mmp) cc_final: 0.8292 (mmp) REVERT: F 292 PHE cc_start: 0.7872 (t80) cc_final: 0.7559 (t80) REVERT: G 266 MET cc_start: 0.6869 (ppp) cc_final: 0.6465 (mmt) REVERT: G 292 PHE cc_start: 0.8053 (t80) cc_final: 0.7644 (t80) REVERT: G 348 ASP cc_start: 0.8796 (m-30) cc_final: 0.8595 (m-30) REVERT: G 410 ASP cc_start: 0.8504 (t0) cc_final: 0.8282 (t0) REVERT: G 416 GLN cc_start: 0.8233 (mp10) cc_final: 0.7876 (mp10) outliers start: 30 outliers final: 6 residues processed: 199 average time/residue: 0.5789 time to fit residues: 126.8665 Evaluate side-chains 185 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 179 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain G residue 316 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 118 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 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 396 GLN A 407 GLN B 407 GLN C 470 GLN E 396 GLN G 407 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.110873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.069514 restraints weight = 27753.621| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.85 r_work: 0.2811 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 14602 Z= 0.218 Angle : 0.677 11.147 19684 Z= 0.331 Chirality : 0.044 0.228 2345 Planarity : 0.003 0.028 2429 Dihedral : 6.027 50.123 2009 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.92 % Allowed : 26.27 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.20), residues: 1806 helix: 1.73 (0.17), residues: 1008 sheet: -0.77 (0.30), residues: 315 loop : -0.90 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 277 TYR 0.023 0.001 TYR C 256 PHE 0.022 0.001 PHE G 254 TRP 0.015 0.001 TRP A 258 HIS 0.003 0.001 HIS B 439 Details of bonding type rmsd covalent geometry : bond 0.00508 (14602) covalent geometry : angle 0.67661 (19684) hydrogen bonds : bond 0.03910 ( 979) hydrogen bonds : angle 4.05782 ( 2901) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 0.569 Fit side-chains REVERT: A 206 TRP cc_start: -0.0698 (m100) cc_final: -0.1169 (p-90) REVERT: A 292 PHE cc_start: 0.7766 (m-80) cc_final: 0.7462 (m-10) REVERT: A 356 GLU cc_start: 0.8330 (tm-30) cc_final: 0.8101 (tm-30) REVERT: A 413 MET cc_start: 0.8602 (mmm) cc_final: 0.8255 (mmm) REVERT: A 416 GLN cc_start: 0.8050 (mp10) cc_final: 0.7805 (mp10) REVERT: B 424 MET cc_start: 0.8848 (tmm) cc_final: 0.8504 (OUTLIER) REVERT: B 468 ASN cc_start: 0.8666 (m-40) cc_final: 0.8282 (m-40) REVERT: C 258 TRP cc_start: 0.7871 (OUTLIER) cc_final: 0.7516 (t-100) REVERT: C 410 ASP cc_start: 0.8273 (t0) cc_final: 0.7984 (t0) REVERT: D 209 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7928 (mm) REVERT: D 228 MET cc_start: 0.5003 (mmp) cc_final: 0.4780 (mmp) REVERT: D 266 MET cc_start: 0.7332 (tmm) cc_final: 0.6960 (ttt) REVERT: D 323 PHE cc_start: 0.8961 (m-10) cc_final: 0.8496 (m-80) REVERT: D 396 GLN cc_start: 0.9005 (mm-40) cc_final: 0.8670 (mm110) REVERT: D 410 ASP cc_start: 0.8565 (t0) cc_final: 0.8232 (t0) REVERT: E 261 ASN cc_start: 0.8067 (m110) cc_final: 0.7585 (m110) REVERT: E 348 ASP cc_start: 0.8845 (m-30) cc_final: 0.8284 (m-30) REVERT: E 356 GLU cc_start: 0.8270 (tm-30) cc_final: 0.8060 (tm-30) REVERT: F 292 PHE cc_start: 0.7810 (t80) cc_final: 0.7506 (t80) REVERT: G 266 MET cc_start: 0.6789 (ppp) cc_final: 0.6560 (mmt) REVERT: G 292 PHE cc_start: 0.8054 (t80) cc_final: 0.7641 (t80) REVERT: G 413 MET cc_start: 0.8650 (mmm) cc_final: 0.8345 (mmm) REVERT: G 416 GLN cc_start: 0.8150 (mp10) cc_final: 0.7734 (mp10) outliers start: 30 outliers final: 10 residues processed: 194 average time/residue: 0.5988 time to fit residues: 127.6307 Evaluate side-chains 184 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 173 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 321 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 32 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 41 optimal weight: 0.0270 chunk 170 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 21 optimal weight: 0.0970 chunk 85 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 407 GLN B 416 GLN C 261 ASN C 339 GLN C 416 GLN E 261 ASN E 381 ASN E 396 GLN F 381 ASN G 407 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.114196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.073075 restraints weight = 27517.219| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.90 r_work: 0.2888 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14602 Z= 0.118 Angle : 0.649 12.535 19684 Z= 0.305 Chirality : 0.042 0.232 2345 Planarity : 0.003 0.029 2429 Dihedral : 5.338 44.637 2009 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.83 % Allowed : 27.35 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.20), residues: 1806 helix: 1.96 (0.17), residues: 1001 sheet: -0.53 (0.31), residues: 315 loop : -0.79 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 326 TYR 0.006 0.001 TYR A 441 PHE 0.024 0.001 PHE G 254 TRP 0.011 0.001 TRP A 258 HIS 0.001 0.000 HIS D 439 Details of bonding type rmsd covalent geometry : bond 0.00250 (14602) covalent geometry : angle 0.64932 (19684) hydrogen bonds : bond 0.03114 ( 979) hydrogen bonds : angle 3.71905 ( 2901) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 178 time to evaluate : 0.625 Fit side-chains REVERT: A 292 PHE cc_start: 0.7791 (m-80) cc_final: 0.7484 (m-10) REVERT: A 413 MET cc_start: 0.8591 (mmm) cc_final: 0.8310 (mmm) REVERT: A 416 GLN cc_start: 0.7872 (mp10) cc_final: 0.7612 (mp10) REVERT: A 424 MET cc_start: 0.8926 (tmm) cc_final: 0.8631 (tmm) REVERT: B 323 PHE cc_start: 0.8924 (m-10) cc_final: 0.8694 (m-80) REVERT: B 416 GLN cc_start: 0.8488 (pt0) cc_final: 0.8177 (pm20) REVERT: B 424 MET cc_start: 0.8963 (tmm) cc_final: 0.8656 (tmm) REVERT: C 410 ASP cc_start: 0.8168 (t0) cc_final: 0.7529 (t0) REVERT: D 228 MET cc_start: 0.4990 (mmp) cc_final: 0.4667 (mpm) REVERT: D 266 MET cc_start: 0.7255 (tmm) cc_final: 0.6940 (ttt) REVERT: D 323 PHE cc_start: 0.8975 (m-10) cc_final: 0.8530 (m-80) REVERT: D 348 ASP cc_start: 0.8744 (m-30) cc_final: 0.8429 (m-30) REVERT: D 396 GLN cc_start: 0.9022 (mm-40) cc_final: 0.8686 (mm110) REVERT: D 410 ASP cc_start: 0.8500 (t0) cc_final: 0.8139 (t0) REVERT: E 261 ASN cc_start: 0.8102 (m-40) cc_final: 0.7565 (m110) REVERT: E 348 ASP cc_start: 0.8748 (m-30) cc_final: 0.8531 (m-30) REVERT: F 292 PHE cc_start: 0.7832 (t80) cc_final: 0.7489 (t80) REVERT: G 266 MET cc_start: 0.6795 (ppp) cc_final: 0.6588 (mmt) REVERT: G 413 MET cc_start: 0.8576 (mmm) cc_final: 0.8295 (mmm) REVERT: G 416 GLN cc_start: 0.8218 (mp10) cc_final: 0.7832 (mp10) outliers start: 13 outliers final: 3 residues processed: 184 average time/residue: 0.5737 time to fit residues: 116.1465 Evaluate side-chains 174 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 171 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain G residue 316 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 29 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 149 optimal weight: 0.6980 chunk 40 optimal weight: 0.0370 chunk 131 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 137 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 overall best weight: 2.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 407 GLN C 358 GLN ** E 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 407 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.111686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.070047 restraints weight = 27809.433| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.90 r_work: 0.2822 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14602 Z= 0.202 Angle : 0.684 12.544 19684 Z= 0.328 Chirality : 0.044 0.240 2345 Planarity : 0.003 0.030 2429 Dihedral : 5.634 46.694 2009 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.90 % Allowed : 27.03 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.21), residues: 1806 helix: 1.90 (0.17), residues: 1008 sheet: -0.56 (0.31), residues: 315 loop : -0.73 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 444 TYR 0.025 0.001 TYR C 256 PHE 0.024 0.001 PHE G 254 TRP 0.013 0.001 TRP A 258 HIS 0.003 0.001 HIS B 439 Details of bonding type rmsd covalent geometry : bond 0.00469 (14602) covalent geometry : angle 0.68398 (19684) hydrogen bonds : bond 0.03646 ( 979) hydrogen bonds : angle 3.93812 ( 2901) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 173 time to evaluate : 0.382 Fit side-chains REVERT: A 292 PHE cc_start: 0.7873 (m-80) cc_final: 0.7583 (m-10) REVERT: A 413 MET cc_start: 0.8602 (mmm) cc_final: 0.8314 (mmm) REVERT: A 416 GLN cc_start: 0.7989 (mp10) cc_final: 0.7710 (mp10) REVERT: B 416 GLN cc_start: 0.8621 (pt0) cc_final: 0.8294 (pm20) REVERT: B 424 MET cc_start: 0.8949 (tmm) cc_final: 0.8624 (OUTLIER) REVERT: B 468 ASN cc_start: 0.8693 (m-40) cc_final: 0.8319 (m-40) REVERT: C 258 TRP cc_start: 0.7838 (OUTLIER) cc_final: 0.7478 (t-100) REVERT: C 410 ASP cc_start: 0.7947 (t0) cc_final: 0.7715 (t0) REVERT: D 228 MET cc_start: 0.4990 (mmp) cc_final: 0.4601 (mpm) REVERT: D 266 MET cc_start: 0.7266 (tmm) cc_final: 0.6959 (ttt) REVERT: D 323 PHE cc_start: 0.8986 (m-10) cc_final: 0.8541 (m-80) REVERT: D 396 GLN cc_start: 0.9044 (mm-40) cc_final: 0.8725 (mm110) REVERT: D 410 ASP cc_start: 0.8455 (t0) cc_final: 0.8095 (t0) REVERT: E 261 ASN cc_start: 0.8196 (m-40) cc_final: 0.7707 (m110) REVERT: E 348 ASP cc_start: 0.8771 (m-30) cc_final: 0.8194 (m-30) REVERT: F 292 PHE cc_start: 0.7868 (t80) cc_final: 0.7642 (m-80) REVERT: F 339 GLN cc_start: 0.9181 (tp-100) cc_final: 0.8931 (mm-40) REVERT: G 413 MET cc_start: 0.8639 (mmm) cc_final: 0.8399 (mmm) REVERT: G 416 GLN cc_start: 0.8158 (mp10) cc_final: 0.7811 (mp10) outliers start: 14 outliers final: 3 residues processed: 181 average time/residue: 0.5848 time to fit residues: 116.2050 Evaluate side-chains 174 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 171 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain G residue 316 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 0.9980 chunk 137 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 142 optimal weight: 0.0050 chunk 147 optimal weight: 5.9990 chunk 95 optimal weight: 0.2980 chunk 128 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 162 optimal weight: 7.9990 chunk 26 optimal weight: 20.0000 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 339 GLN ** C 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 396 GLN G 407 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.113014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.071672 restraints weight = 27471.230| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.92 r_work: 0.2856 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14602 Z= 0.134 Angle : 0.659 11.649 19684 Z= 0.313 Chirality : 0.042 0.228 2345 Planarity : 0.003 0.029 2429 Dihedral : 5.375 43.285 2009 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.32 % Allowed : 27.67 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.20), residues: 1806 helix: 2.07 (0.17), residues: 980 sheet: -0.33 (0.31), residues: 308 loop : -0.66 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 265 TYR 0.007 0.001 TYR C 256 PHE 0.022 0.001 PHE E 323 TRP 0.012 0.001 TRP A 258 HIS 0.002 0.000 HIS D 439 Details of bonding type rmsd covalent geometry : bond 0.00293 (14602) covalent geometry : angle 0.65946 (19684) hydrogen bonds : bond 0.03276 ( 979) hydrogen bonds : angle 3.80502 ( 2901) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 173 time to evaluate : 0.543 Fit side-chains REVERT: A 258 TRP cc_start: 0.7271 (t-100) cc_final: 0.7049 (t-100) REVERT: A 292 PHE cc_start: 0.7871 (m-80) cc_final: 0.7593 (m-10) REVERT: A 413 MET cc_start: 0.8590 (mmm) cc_final: 0.8300 (mmm) REVERT: A 416 GLN cc_start: 0.7964 (mp10) cc_final: 0.7704 (mp10) REVERT: A 424 MET cc_start: 0.8933 (tmm) cc_final: 0.8689 (tmm) REVERT: B 416 GLN cc_start: 0.8562 (pt0) cc_final: 0.8242 (pm20) REVERT: B 424 MET cc_start: 0.8971 (tmm) cc_final: 0.8663 (tmm) REVERT: C 410 ASP cc_start: 0.8298 (t0) cc_final: 0.8055 (t0) REVERT: D 228 MET cc_start: 0.4947 (mmp) cc_final: 0.4599 (mpm) REVERT: D 266 MET cc_start: 0.7238 (tmm) cc_final: 0.6903 (ttt) REVERT: D 323 PHE cc_start: 0.8990 (m-10) cc_final: 0.8576 (m-80) REVERT: D 348 ASP cc_start: 0.8780 (m-30) cc_final: 0.8473 (m-30) REVERT: D 396 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8694 (mm110) REVERT: D 410 ASP cc_start: 0.8465 (t0) cc_final: 0.8107 (t0) REVERT: D 416 GLN cc_start: 0.8702 (pt0) cc_final: 0.8305 (pm20) REVERT: E 348 ASP cc_start: 0.8773 (m-30) cc_final: 0.8418 (m-30) REVERT: G 413 MET cc_start: 0.8618 (mmm) cc_final: 0.8375 (mmm) REVERT: G 416 GLN cc_start: 0.8169 (mp10) cc_final: 0.7832 (mp10) outliers start: 5 outliers final: 3 residues processed: 174 average time/residue: 0.6245 time to fit residues: 118.9129 Evaluate side-chains 174 residues out of total 1561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 171 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 346 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 15 optimal weight: 0.0070 chunk 108 optimal weight: 6.9990 chunk 161 optimal weight: 20.0000 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 96 optimal weight: 0.0770 chunk 181 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 173 optimal weight: 0.6980 chunk 115 optimal weight: 0.0870 overall best weight: 0.3334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN B 261 ASN B 407 GLN ** C 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 261 ASN G 261 ASN G 407 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.115098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.074049 restraints weight = 27691.331| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.88 r_work: 0.2903 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14602 Z= 0.113 Angle : 0.643 12.225 19684 Z= 0.304 Chirality : 0.041 0.225 2345 Planarity : 0.003 0.030 2429 Dihedral : 4.943 34.637 2009 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.77 % Allowed : 26.91 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.21), residues: 1806 helix: 2.04 (0.17), residues: 1001 sheet: -0.22 (0.31), residues: 308 loop : -0.51 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 326 TYR 0.005 0.000 TYR C 256 PHE 0.042 0.001 PHE E 323 TRP 0.012 0.001 TRP A 258 HIS 0.001 0.000 HIS A 439 Details of bonding type rmsd covalent geometry : bond 0.00237 (14602) covalent geometry : angle 0.64347 (19684) hydrogen bonds : bond 0.02941 ( 979) hydrogen bonds : angle 3.65912 ( 2901) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5066.66 seconds wall clock time: 86 minutes 56.82 seconds (5216.82 seconds total)