Starting phenix.real_space_refine on Fri Sep 27 00:24:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxn_21445/09_2024/6vxn_21445.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxn_21445/09_2024/6vxn_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxn_21445/09_2024/6vxn_21445.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxn_21445/09_2024/6vxn_21445.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxn_21445/09_2024/6vxn_21445.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxn_21445/09_2024/6vxn_21445.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 8.14, per 1000 atoms: 0.57 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: 3.41 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.52 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: 4.25 Time building geometry restraints manager: 3.97 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 204 through 491) selection = (chain 'C' and resid 204 through 491) selection = (chain 'D' and resid 204 through 491) selection = chain 'E' selection = (chain 'F' and resid 204 through 491) selection = (chain 'G' and resid 204 through 491) } 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: 0.830 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: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 32.220 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 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:10.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.690 ------------------------------------------------------------------------------- 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= 0.864 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.022 0.003 TRP G 206 HIS 0.003 0.001 HIS C 439 PHE 0.017 0.002 PHE E 384 TYR 0.012 0.002 TYR F 441 ARG 0.007 0.001 ARG G 444 *********************** 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 fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 1.655 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: 0.8735 (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: 1.3709 time to fit residues: 460.7239 Evaluate side-chains 192 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 188 time to evaluate : 1.707 ------------------------------------------------------------------------------- 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 153 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 106 optimal weight: 0.2980 chunk 165 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14602 Z= 0.240 Angle : 0.664 8.748 19684 Z= 0.331 Chirality : 0.044 0.228 2345 Planarity : 0.005 0.035 2429 Dihedral : 8.072 119.375 2017 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.86 % Allowed : 21.78 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.19), residues: 1806 helix: 0.31 (0.16), residues: 1008 sheet: -1.63 (0.25), residues: 350 loop : -1.73 (0.24), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 206 HIS 0.002 0.001 HIS D 439 PHE 0.016 0.001 PHE G 254 TYR 0.017 0.001 TYR F 256 ARG 0.012 0.001 ARG A 342 *********************** 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 236 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 207 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 TRP cc_start: 0.0173 (m100) cc_final: -0.0299 (p90) REVERT: A 258 TRP cc_start: 0.8388 (t60) cc_final: 0.8098 (t60) REVERT: A 266 MET cc_start: 0.7184 (ppp) cc_final: 0.6814 (mmt) REVERT: C 254 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8377 (t80) REVERT: C 292 PHE cc_start: 0.7901 (t80) cc_final: 0.7691 (t80) REVERT: D 228 MET cc_start: 0.5076 (mmp) cc_final: 0.4623 (mmp) REVERT: D 266 MET cc_start: 0.7436 (tmm) cc_final: 0.6888 (ttt) REVERT: D 319 VAL cc_start: 0.8666 (t) cc_final: 0.8174 (m) REVERT: D 323 PHE cc_start: 0.8857 (m-10) cc_final: 0.8598 (m-80) REVERT: D 339 GLN cc_start: 0.8975 (mm-40) cc_final: 0.8748 (tp40) REVERT: E 224 GLN cc_start: 0.7788 (tp-100) cc_final: 0.7350 (tt0) REVERT: E 339 GLN cc_start: 0.8788 (mm-40) cc_final: 0.8421 (mm-40) REVERT: F 266 MET cc_start: 0.7038 (pp-130) cc_final: 0.6822 (mmt) REVERT: F 292 PHE cc_start: 0.8064 (t80) cc_final: 0.7798 (t80) REVERT: F 410 ASP cc_start: 0.7672 (t0) cc_final: 0.7359 (t0) REVERT: F 482 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8300 (mttt) REVERT: G 266 MET cc_start: 0.7068 (ppp) cc_final: 0.6488 (mmt) REVERT: G 292 PHE cc_start: 0.7896 (t80) cc_final: 0.7490 (t80) outliers start: 29 outliers final: 10 residues processed: 219 average time/residue: 1.1051 time to fit residues: 268.8038 Evaluate side-chains 193 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 181 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 GLN Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain D residue 243 VAL 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 Chi-restraints excluded: chain G residue 346 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 112 optimal weight: 30.0000 chunk 45 optimal weight: 0.4980 chunk 165 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 132 optimal weight: 0.0050 overall best weight: 1.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 ASN A 407 GLN C 339 GLN C 358 GLN C 381 ASN D 407 GLN E 407 GLN G 407 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14602 Z= 0.216 Angle : 0.631 9.052 19684 Z= 0.311 Chirality : 0.043 0.213 2345 Planarity : 0.004 0.035 2429 Dihedral : 6.401 51.561 2009 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.31 % Allowed : 23.00 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.20), residues: 1806 helix: 1.17 (0.17), residues: 1008 sheet: -1.48 (0.26), residues: 350 loop : -1.38 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 206 HIS 0.002 0.001 HIS B 439 PHE 0.033 0.001 PHE B 323 TYR 0.015 0.001 TYR C 256 ARG 0.006 0.001 ARG A 342 *********************** 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 228 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 192 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 TRP cc_start: 0.0004 (m100) cc_final: -0.0470 (p90) REVERT: A 258 TRP cc_start: 0.8383 (t60) cc_final: 0.8081 (t60) REVERT: A 266 MET cc_start: 0.7014 (ppp) cc_final: 0.6741 (mmt) REVERT: C 254 PHE cc_start: 0.8592 (OUTLIER) cc_final: 0.8347 (t80) REVERT: C 278 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8098 (tm-30) REVERT: C 292 PHE cc_start: 0.7908 (t80) cc_final: 0.7674 (t80) REVERT: D 228 MET cc_start: 0.5215 (mmp) cc_final: 0.4902 (mmp) REVERT: D 266 MET cc_start: 0.7531 (tmm) cc_final: 0.7053 (ttt) REVERT: D 319 VAL cc_start: 0.8622 (t) cc_final: 0.8142 (m) REVERT: D 323 PHE cc_start: 0.8866 (m-10) cc_final: 0.8614 (m-80) REVERT: E 258 TRP cc_start: 0.8085 (OUTLIER) cc_final: 0.7476 (t-100) REVERT: E 339 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8211 (mm-40) REVERT: F 292 PHE cc_start: 0.8024 (t80) cc_final: 0.7747 (t80) REVERT: F 482 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8342 (mttt) REVERT: G 266 MET cc_start: 0.6938 (ppp) cc_final: 0.6451 (mmt) REVERT: G 292 PHE cc_start: 0.7916 (t80) cc_final: 0.7486 (t80) outliers start: 36 outliers final: 10 residues processed: 208 average time/residue: 1.0871 time to fit residues: 251.3603 Evaluate side-chains 189 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 175 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain E residue 258 TRP Chi-restraints excluded: chain E residue 362 MET 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 316 VAL 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 163 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 166 optimal weight: 3.9990 chunk 175 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 396 GLN A 407 GLN B 407 GLN F 381 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3574 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= 0.312 Angle : 0.662 9.181 19684 Z= 0.329 Chirality : 0.044 0.248 2345 Planarity : 0.004 0.033 2429 Dihedral : 6.397 53.774 2009 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.75 % Allowed : 23.57 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.20), residues: 1806 helix: 1.44 (0.17), residues: 1008 sheet: -1.11 (0.29), residues: 315 loop : -1.25 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 206 HIS 0.003 0.001 HIS B 439 PHE 0.021 0.001 PHE B 323 TYR 0.006 0.001 TYR A 441 ARG 0.004 0.000 ARG E 326 *********************** 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 229 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 186 time to evaluate : 1.666 Fit side-chains REVERT: A 206 TRP cc_start: 0.0112 (m100) cc_final: -0.0506 (p90) REVERT: A 258 TRP cc_start: 0.8329 (t60) cc_final: 0.8020 (t60) REVERT: A 266 MET cc_start: 0.7077 (ppp) cc_final: 0.6786 (mmt) REVERT: A 292 PHE cc_start: 0.7793 (m-80) cc_final: 0.7519 (m-80) REVERT: C 278 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7945 (tm-30) REVERT: C 410 ASP cc_start: 0.7399 (t0) cc_final: 0.7092 (t0) REVERT: D 228 MET cc_start: 0.5204 (mmp) cc_final: 0.4945 (mmp) REVERT: D 266 MET cc_start: 0.7566 (tmm) cc_final: 0.7085 (ttt) REVERT: D 319 VAL cc_start: 0.8598 (t) cc_final: 0.8185 (m) REVERT: D 323 PHE cc_start: 0.8897 (m-10) cc_final: 0.8634 (m-80) REVERT: E 258 TRP cc_start: 0.8082 (OUTLIER) cc_final: 0.7483 (t-100) REVERT: E 261 ASN cc_start: 0.8307 (m110) cc_final: 0.7805 (m110) REVERT: E 339 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8261 (mm-40) REVERT: F 292 PHE cc_start: 0.7991 (t80) cc_final: 0.7678 (t80) REVERT: F 482 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8415 (mttt) REVERT: G 266 MET cc_start: 0.7090 (ppp) cc_final: 0.6690 (mmt) REVERT: G 292 PHE cc_start: 0.8030 (t80) cc_final: 0.7568 (t80) outliers start: 43 outliers final: 15 residues processed: 209 average time/residue: 1.1073 time to fit residues: 257.0218 Evaluate side-chains 191 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 173 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 387 GLN Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 258 TRP 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 387 GLN Chi-restraints excluded: chain F residue 482 LYS 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 146 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 130 optimal weight: 20.0000 chunk 72 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 89 optimal weight: 0.9990 chunk 157 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 D 381 ASN D 407 GLN E 381 ASN E 396 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3764 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= 0.213 Angle : 0.647 9.750 19684 Z= 0.314 Chirality : 0.043 0.240 2345 Planarity : 0.003 0.034 2429 Dihedral : 6.067 54.222 2009 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.60 % Allowed : 25.88 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.20), residues: 1806 helix: 1.61 (0.17), residues: 1001 sheet: -0.96 (0.29), residues: 315 loop : -1.10 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 258 HIS 0.002 0.001 HIS B 439 PHE 0.019 0.001 PHE G 254 TYR 0.017 0.001 TYR C 256 ARG 0.004 0.000 ARG E 326 *********************** 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 204 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 179 time to evaluate : 1.690 Fit side-chains REVERT: A 206 TRP cc_start: 0.0043 (m100) cc_final: -0.0543 (p90) REVERT: A 258 TRP cc_start: 0.8331 (t60) cc_final: 0.8020 (t60) REVERT: A 266 MET cc_start: 0.7082 (ppp) cc_final: 0.6767 (mmt) REVERT: C 278 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7922 (tm-30) REVERT: D 228 MET cc_start: 0.5205 (mmp) cc_final: 0.4983 (mmp) REVERT: D 266 MET cc_start: 0.7503 (tmm) cc_final: 0.7005 (ttt) REVERT: D 319 VAL cc_start: 0.8587 (t) cc_final: 0.8213 (m) REVERT: E 261 ASN cc_start: 0.8292 (m110) cc_final: 0.7791 (m110) REVERT: E 339 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8246 (mm-40) REVERT: F 292 PHE cc_start: 0.7955 (t80) cc_final: 0.7623 (t80) REVERT: F 482 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8384 (mttt) REVERT: G 266 MET cc_start: 0.6999 (ppp) cc_final: 0.6605 (mmt) REVERT: G 292 PHE cc_start: 0.8022 (t80) cc_final: 0.7543 (t80) outliers start: 25 outliers final: 8 residues processed: 196 average time/residue: 1.1931 time to fit residues: 258.1339 Evaluate side-chains 182 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 172 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain F residue 482 LYS Chi-restraints excluded: chain G residue 316 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 5.9990 chunk 158 optimal weight: 9.9990 chunk 34 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 146 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 14 optimal weight: 0.0170 chunk 58 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.1020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 GLN B 407 GLN C 339 GLN D 407 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14602 Z= 0.181 Angle : 0.639 11.355 19684 Z= 0.309 Chirality : 0.042 0.226 2345 Planarity : 0.003 0.030 2429 Dihedral : 5.789 53.200 2009 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.67 % Allowed : 27.03 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.20), residues: 1806 helix: 1.68 (0.17), residues: 1001 sheet: -0.84 (0.30), residues: 315 loop : -1.01 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 258 HIS 0.002 0.000 HIS B 439 PHE 0.038 0.001 PHE D 323 TYR 0.005 0.001 TYR A 441 ARG 0.004 0.000 ARG G 342 *********************** 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 206 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 180 time to evaluate : 1.742 Fit side-chains REVERT: A 206 TRP cc_start: -0.0165 (m100) cc_final: -0.0731 (p90) REVERT: A 258 TRP cc_start: 0.8269 (t60) cc_final: 0.7973 (t60) REVERT: A 266 MET cc_start: 0.7006 (ppp) cc_final: 0.6721 (mmt) REVERT: A 292 PHE cc_start: 0.7781 (m-80) cc_final: 0.7450 (m-10) REVERT: C 416 GLN cc_start: 0.6897 (pm20) cc_final: 0.5398 (pm20) REVERT: D 228 MET cc_start: 0.5159 (mmp) cc_final: 0.4870 (mmp) REVERT: D 266 MET cc_start: 0.7447 (tmm) cc_final: 0.7020 (ttt) REVERT: E 261 ASN cc_start: 0.8228 (m110) cc_final: 0.7727 (m110) REVERT: E 339 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8188 (mm-40) REVERT: F 254 PHE cc_start: 0.8642 (t80) cc_final: 0.8414 (t80) REVERT: F 292 PHE cc_start: 0.7891 (t80) cc_final: 0.7560 (t80) REVERT: F 482 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8411 (mttt) REVERT: G 292 PHE cc_start: 0.8054 (t80) cc_final: 0.7569 (t80) outliers start: 26 outliers final: 15 residues processed: 195 average time/residue: 1.1472 time to fit residues: 247.4664 Evaluate side-chains 186 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 170 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 482 LYS Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 346 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 148 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 175 optimal weight: 0.6980 chunk 109 optimal weight: 8.9990 chunk 106 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 C 339 GLN E 396 GLN G 407 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14602 Z= 0.175 Angle : 0.648 12.422 19684 Z= 0.309 Chirality : 0.042 0.221 2345 Planarity : 0.003 0.027 2429 Dihedral : 5.538 50.546 2009 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.86 % Allowed : 27.03 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.20), residues: 1806 helix: 1.77 (0.17), residues: 1001 sheet: -0.63 (0.30), residues: 308 loop : -0.99 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 258 HIS 0.002 0.000 HIS D 439 PHE 0.037 0.001 PHE D 323 TYR 0.017 0.001 TYR C 256 ARG 0.003 0.000 ARG E 326 *********************** 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 198 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 169 time to evaluate : 1.664 Fit side-chains REVERT: A 206 TRP cc_start: -0.0210 (m100) cc_final: -0.1058 (p90) REVERT: A 258 TRP cc_start: 0.8263 (t60) cc_final: 0.7967 (t60) REVERT: A 266 MET cc_start: 0.6864 (ppp) cc_final: 0.6653 (mmt) REVERT: A 292 PHE cc_start: 0.7912 (m-80) cc_final: 0.7571 (m-10) REVERT: D 228 MET cc_start: 0.5150 (mmp) cc_final: 0.4857 (mmp) REVERT: D 266 MET cc_start: 0.7382 (tmm) cc_final: 0.6934 (ttt) REVERT: E 261 ASN cc_start: 0.8251 (m110) cc_final: 0.7743 (m110) REVERT: E 339 GLN cc_start: 0.8597 (mm-40) cc_final: 0.8187 (mm-40) REVERT: F 292 PHE cc_start: 0.7916 (t80) cc_final: 0.7540 (t80) REVERT: F 482 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8418 (mttt) REVERT: G 292 PHE cc_start: 0.8047 (t80) cc_final: 0.7560 (t80) outliers start: 29 outliers final: 15 residues processed: 186 average time/residue: 1.1501 time to fit residues: 236.9239 Evaluate side-chains 182 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 166 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 482 LYS Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 346 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 104 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 119 optimal weight: 0.0670 chunk 86 optimal weight: 20.0000 chunk 16 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 overall best weight: 2.8124 ------------------------------------------------------------------------------- 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 G 407 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 14602 Z= 0.348 Angle : 0.710 13.447 19684 Z= 0.343 Chirality : 0.045 0.224 2345 Planarity : 0.003 0.028 2429 Dihedral : 6.032 53.460 2009 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.79 % Allowed : 27.35 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.20), residues: 1806 helix: 1.68 (0.17), residues: 1008 sheet: -0.71 (0.30), residues: 308 loop : -0.97 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 258 HIS 0.004 0.001 HIS B 439 PHE 0.035 0.001 PHE D 323 TYR 0.007 0.001 TYR G 441 ARG 0.002 0.000 ARG G 342 *********************** 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 196 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 168 time to evaluate : 1.868 Fit side-chains REVERT: A 206 TRP cc_start: -0.0203 (m100) cc_final: -0.1107 (p90) REVERT: A 258 TRP cc_start: 0.8288 (t60) cc_final: 0.7985 (t60) REVERT: A 292 PHE cc_start: 0.7912 (m-80) cc_final: 0.7592 (m-10) REVERT: C 258 TRP cc_start: 0.8227 (OUTLIER) cc_final: 0.7724 (t-100) REVERT: C 292 PHE cc_start: 0.7730 (m-80) cc_final: 0.7263 (m-10) REVERT: D 228 MET cc_start: 0.5173 (mmp) cc_final: 0.4961 (mmp) REVERT: D 266 MET cc_start: 0.7374 (tmm) cc_final: 0.6944 (ttt) REVERT: E 339 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8431 (mm-40) REVERT: F 292 PHE cc_start: 0.7931 (t80) cc_final: 0.7714 (m-80) REVERT: F 482 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8417 (mttt) outliers start: 28 outliers final: 14 residues processed: 182 average time/residue: 1.2261 time to fit residues: 247.0534 Evaluate side-chains 181 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 165 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain F residue 482 LYS Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain G residue 346 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 163 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 154 optimal weight: 0.9990 chunk 162 optimal weight: 7.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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 C 339 GLN E 396 GLN G 407 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14602 Z= 0.195 Angle : 0.691 14.259 19684 Z= 0.326 Chirality : 0.042 0.223 2345 Planarity : 0.003 0.027 2429 Dihedral : 5.688 51.558 2009 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.22 % Allowed : 27.93 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.20), residues: 1806 helix: 1.86 (0.17), residues: 1001 sheet: -0.60 (0.31), residues: 308 loop : -0.87 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 258 HIS 0.002 0.000 HIS D 439 PHE 0.033 0.001 PHE D 323 TYR 0.009 0.001 TYR C 256 ARG 0.003 0.000 ARG G 342 *********************** 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 fitting. rotamer outliers: 19 poor density : 168 time to evaluate : 1.749 Fit side-chains REVERT: A 258 TRP cc_start: 0.8275 (t60) cc_final: 0.7981 (t60) REVERT: A 292 PHE cc_start: 0.7881 (m-80) cc_final: 0.7584 (m-10) REVERT: C 292 PHE cc_start: 0.7767 (m-80) cc_final: 0.7332 (m-10) REVERT: D 228 MET cc_start: 0.5122 (mmp) cc_final: 0.4842 (mmp) REVERT: D 266 MET cc_start: 0.7383 (tmm) cc_final: 0.6952 (ttt) REVERT: E 339 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8195 (mm-40) REVERT: F 206 TRP cc_start: -0.0106 (m100) cc_final: -0.0740 (p-90) REVERT: F 292 PHE cc_start: 0.8003 (t80) cc_final: 0.7800 (m-80) outliers start: 19 outliers final: 11 residues processed: 180 average time/residue: 1.1625 time to fit residues: 231.1899 Evaluate side-chains 177 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 166 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain E residue 316 VAL 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 107 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 120 optimal weight: 0.4980 chunk 181 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 C 339 GLN G 407 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14602 Z= 0.233 Angle : 0.695 13.990 19684 Z= 0.333 Chirality : 0.043 0.226 2345 Planarity : 0.003 0.029 2429 Dihedral : 5.680 50.613 2009 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.22 % Allowed : 27.99 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.20), residues: 1806 helix: 1.85 (0.17), residues: 1001 sheet: -0.58 (0.31), residues: 308 loop : -0.83 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 258 HIS 0.002 0.001 HIS B 439 PHE 0.033 0.001 PHE D 323 TYR 0.005 0.001 TYR F 441 ARG 0.003 0.000 ARG G 342 ********************** 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 186 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 167 time to evaluate : 1.556 Fit side-chains REVERT: A 258 TRP cc_start: 0.8282 (t60) cc_final: 0.7985 (t60) REVERT: A 292 PHE cc_start: 0.7890 (m-80) cc_final: 0.7594 (m-10) REVERT: C 292 PHE cc_start: 0.7766 (m-80) cc_final: 0.7313 (m-10) REVERT: D 228 MET cc_start: 0.5196 (mmp) cc_final: 0.4994 (mmp) REVERT: D 266 MET cc_start: 0.7385 (tmm) cc_final: 0.6953 (ttt) REVERT: E 339 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8220 (mm-40) REVERT: F 206 TRP cc_start: -0.0205 (m100) cc_final: -0.0581 (p-90) outliers start: 19 outliers final: 11 residues processed: 179 average time/residue: 1.1219 time to fit residues: 223.1463 Evaluate side-chains 176 residues out of total 1561 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 165 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain E residue 316 VAL Chi-restraints excluded: chain F residue 316 VAL 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 114 optimal weight: 2.9990 chunk 153 optimal weight: 0.3980 chunk 44 optimal weight: 0.0770 chunk 133 optimal weight: 3.9990 chunk 21 optimal weight: 0.3980 chunk 40 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 60 optimal weight: 0.0020 chunk 148 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 overall best weight: 0.3546 ------------------------------------------------------------------------------- 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 C 261 ASN C 419 ASN E 261 ASN E 396 GLN F 261 ASN G 407 GLN G 470 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.114182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.073129 restraints weight = 27645.887| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.88 r_work: 0.2893 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14602 Z= 0.155 Angle : 0.684 13.245 19684 Z= 0.322 Chirality : 0.042 0.220 2345 Planarity : 0.003 0.028 2429 Dihedral : 5.192 42.031 2009 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.90 % Allowed : 28.06 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.20), residues: 1806 helix: 1.97 (0.17), residues: 994 sheet: -0.42 (0.31), residues: 308 loop : -0.70 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 258 HIS 0.001 0.000 HIS D 439 PHE 0.031 0.001 PHE D 323 TYR 0.004 0.000 TYR F 441 ARG 0.003 0.000 ARG E 326 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4852.86 seconds wall clock time: 85 minutes 44.90 seconds (5144.90 seconds total)