Starting phenix.real_space_refine on Sat Mar 16 19:06:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq6_25377/03_2024/7sq6_25377_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq6_25377/03_2024/7sq6_25377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq6_25377/03_2024/7sq6_25377.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq6_25377/03_2024/7sq6_25377.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq6_25377/03_2024/7sq6_25377_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq6_25377/03_2024/7sq6_25377_neut_trim_updated.pdb" } resolution = 2.32 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 96 5.16 5 Na 2 4.78 5 C 10064 2.51 5 N 2532 2.21 5 O 2648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 61": "NH1" <-> "NH2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "B ARG 61": "NH1" <-> "NH2" Residue "B GLU 141": "OE1" <-> "OE2" Residue "B GLU 276": "OE1" <-> "OE2" Residue "C ARG 61": "NH1" <-> "NH2" Residue "C GLU 141": "OE1" <-> "OE2" Residue "C GLU 276": "OE1" <-> "OE2" Residue "D ARG 61": "NH1" <-> "NH2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D GLU 276": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15342 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3777 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 14, 'TRANS': 452} Chain breaks: 2 Chain: "B" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3777 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 14, 'TRANS': 452} Chain breaks: 2 Chain: "C" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3777 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 14, 'TRANS': 452} Chain breaks: 2 Chain: "D" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3777 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 14, 'TRANS': 452} Chain breaks: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' NA': 1, 'AQV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'AQV': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' NA': 1, 'AQV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'AQV': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 8.42, per 1000 atoms: 0.55 Number of scatterers: 15342 At special positions: 0 Unit cell: (108.73, 108.73, 110.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 Na 2 11.00 O 2648 8.00 N 2532 7.00 C 10064 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 - 3.50 Amino acid : False - 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG E 1 " - " ASN A 230 " " NAG F 1 " - " ASN B 230 " " NAG G 1 " - " ASN C 230 " " NAG H 1 " - " ASN D 230 " Time building additional restraints: 6.58 Conformation dependent library (CDL) restraints added in 3.0 seconds 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3536 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 4 sheets defined 61.7% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.89 Creating SS restraints... Processing helix chain 'A' and resid 43 through 48 Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 64 through 105 removed outlier: 3.586A pdb=" N VAL A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 142 Proline residue: A 140 - end of helix Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 298 through 337 Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 353 through 376 Processing helix chain 'A' and resid 383 through 405 removed outlier: 3.785A pdb=" N VAL A 401 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE A 402 " --> pdb=" O TRP A 398 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ARG A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU A 405 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 411 No H-bonds generated for 'chain 'A' and resid 409 through 411' Processing helix chain 'A' and resid 413 through 446 Proline residue: A 423 - end of helix removed outlier: 3.627A pdb=" N CYS A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 434 " --> pdb=" O CYS A 430 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE A 435 " --> pdb=" O CYS A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 457 through 468 Processing helix chain 'A' and resid 473 through 486 removed outlier: 3.823A pdb=" N MET A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLY A 485 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N HIS A 486 " --> pdb=" O ALA A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 507 Processing helix chain 'A' and resid 509 through 524 Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 52 through 59 Processing helix chain 'B' and resid 64 through 105 removed outlier: 3.585A pdb=" N VAL B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 142 Proline residue: B 140 - end of helix Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 242 through 247 Processing helix chain 'B' and resid 298 through 337 Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 353 through 376 Processing helix chain 'B' and resid 383 through 405 removed outlier: 3.785A pdb=" N VAL B 401 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE B 402 " --> pdb=" O TRP B 398 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ARG B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR B 404 " --> pdb=" O GLY B 400 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU B 405 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 411 No H-bonds generated for 'chain 'B' and resid 409 through 411' Processing helix chain 'B' and resid 413 through 446 Proline residue: B 423 - end of helix removed outlier: 3.627A pdb=" N CYS B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL B 434 " --> pdb=" O CYS B 430 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE B 435 " --> pdb=" O CYS B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 454 No H-bonds generated for 'chain 'B' and resid 452 through 454' Processing helix chain 'B' and resid 457 through 468 Processing helix chain 'B' and resid 473 through 486 removed outlier: 3.823A pdb=" N MET B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLY B 485 " --> pdb=" O GLN B 481 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N HIS B 486 " --> pdb=" O ALA B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 507 Processing helix chain 'B' and resid 509 through 524 Processing helix chain 'C' and resid 43 through 48 Processing helix chain 'C' and resid 52 through 59 Processing helix chain 'C' and resid 64 through 105 removed outlier: 3.585A pdb=" N VAL C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 142 Proline residue: C 140 - end of helix Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 217 through 220 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 298 through 337 Processing helix chain 'C' and resid 345 through 350 Processing helix chain 'C' and resid 353 through 376 Processing helix chain 'C' and resid 383 through 405 removed outlier: 3.785A pdb=" N VAL C 401 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE C 402 " --> pdb=" O TRP C 398 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ARG C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU C 405 " --> pdb=" O VAL C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 411 No H-bonds generated for 'chain 'C' and resid 409 through 411' Processing helix chain 'C' and resid 413 through 446 Proline residue: C 423 - end of helix removed outlier: 3.627A pdb=" N CYS C 431 " --> pdb=" O ARG C 427 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL C 434 " --> pdb=" O CYS C 430 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE C 435 " --> pdb=" O CYS C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 454 No H-bonds generated for 'chain 'C' and resid 452 through 454' Processing helix chain 'C' and resid 457 through 468 Processing helix chain 'C' and resid 473 through 486 removed outlier: 3.823A pdb=" N MET C 480 " --> pdb=" O THR C 476 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLY C 485 " --> pdb=" O GLN C 481 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N HIS C 486 " --> pdb=" O ALA C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 507 Processing helix chain 'C' and resid 509 through 524 Processing helix chain 'D' and resid 43 through 48 Processing helix chain 'D' and resid 52 through 59 Processing helix chain 'D' and resid 64 through 105 removed outlier: 3.586A pdb=" N VAL D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 142 Proline residue: D 140 - end of helix Processing helix chain 'D' and resid 177 through 179 No H-bonds generated for 'chain 'D' and resid 177 through 179' Processing helix chain 'D' and resid 217 through 220 Processing helix chain 'D' and resid 225 through 227 No H-bonds generated for 'chain 'D' and resid 225 through 227' Processing helix chain 'D' and resid 242 through 247 Processing helix chain 'D' and resid 298 through 337 Processing helix chain 'D' and resid 345 through 350 Processing helix chain 'D' and resid 353 through 376 Processing helix chain 'D' and resid 383 through 405 removed outlier: 3.785A pdb=" N VAL D 401 " --> pdb=" O VAL D 397 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE D 402 " --> pdb=" O TRP D 398 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ARG D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR D 404 " --> pdb=" O GLY D 400 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU D 405 " --> pdb=" O VAL D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 411 No H-bonds generated for 'chain 'D' and resid 409 through 411' Processing helix chain 'D' and resid 413 through 446 Proline residue: D 423 - end of helix removed outlier: 3.626A pdb=" N CYS D 431 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D 434 " --> pdb=" O CYS D 430 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE D 435 " --> pdb=" O CYS D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 454 No H-bonds generated for 'chain 'D' and resid 452 through 454' Processing helix chain 'D' and resid 457 through 468 Processing helix chain 'D' and resid 473 through 486 removed outlier: 3.823A pdb=" N MET D 480 " --> pdb=" O THR D 476 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN D 483 " --> pdb=" O ALA D 479 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLY D 485 " --> pdb=" O GLN D 481 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N HIS D 486 " --> pdb=" O ALA D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 507 Processing helix chain 'D' and resid 509 through 524 Processing sheet with id= A, first strand: chain 'A' and resid 188 through 195 removed outlier: 6.390A pdb=" N TYR A 170 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU A 228 " --> pdb=" O TYR A 170 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 188 through 195 removed outlier: 6.389A pdb=" N TYR B 170 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU B 228 " --> pdb=" O TYR B 170 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 188 through 195 removed outlier: 6.390A pdb=" N TYR C 170 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU C 228 " --> pdb=" O TYR C 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 188 through 195 removed outlier: 6.390A pdb=" N TYR D 170 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU D 228 " --> pdb=" O TYR D 170 " (cutoff:3.500A) 932 hydrogen bonds defined for protein. 2724 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: 4.59 Time building geometry restraints manager: 7.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2280 1.31 - 1.44: 4596 1.44 - 1.57: 8700 1.57 - 1.70: 4 1.70 - 1.83: 132 Bond restraints: 15712 Sorted by residual: bond pdb=" C15 AQV A 601 " pdb=" N2 AQV A 601 " ideal model delta sigma weight residual 1.423 1.543 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C15 AQV D 601 " pdb=" N2 AQV D 601 " ideal model delta sigma weight residual 1.423 1.543 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C15 AQV C 601 " pdb=" N2 AQV C 601 " ideal model delta sigma weight residual 1.423 1.543 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C15 AQV B 601 " pdb=" N2 AQV B 601 " ideal model delta sigma weight residual 1.423 1.543 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" C10 AQV D 601 " pdb=" N2 AQV D 601 " ideal model delta sigma weight residual 1.367 1.482 -0.115 2.00e-02 2.50e+03 3.29e+01 ... (remaining 15707 not shown) Histogram of bond angle deviations from ideal: 100.12 - 106.89: 387 106.89 - 113.66: 8699 113.66 - 120.43: 6326 120.43 - 127.20: 5768 127.20 - 133.97: 152 Bond angle restraints: 21332 Sorted by residual: angle pdb=" CA LEU B 348 " pdb=" C LEU B 348 " pdb=" O LEU B 348 " ideal model delta sigma weight residual 121.00 116.82 4.18 1.05e+00 9.07e-01 1.59e+01 angle pdb=" CA LEU A 348 " pdb=" C LEU A 348 " pdb=" O LEU A 348 " ideal model delta sigma weight residual 121.00 116.84 4.16 1.05e+00 9.07e-01 1.57e+01 angle pdb=" CA LEU D 348 " pdb=" C LEU D 348 " pdb=" O LEU D 348 " ideal model delta sigma weight residual 121.00 116.84 4.16 1.05e+00 9.07e-01 1.57e+01 angle pdb=" CA LEU C 348 " pdb=" C LEU C 348 " pdb=" O LEU C 348 " ideal model delta sigma weight residual 121.00 116.84 4.16 1.05e+00 9.07e-01 1.57e+01 angle pdb=" N ARG A 347 " pdb=" CA ARG A 347 " pdb=" C ARG A 347 " ideal model delta sigma weight residual 111.11 106.45 4.66 1.20e+00 6.94e-01 1.51e+01 ... (remaining 21327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 8160 17.97 - 35.94: 908 35.94 - 53.92: 176 53.92 - 71.89: 48 71.89 - 89.86: 32 Dihedral angle restraints: 9324 sinusoidal: 3840 harmonic: 5484 Sorted by residual: dihedral pdb=" C VAL C 332 " pdb=" N VAL C 332 " pdb=" CA VAL C 332 " pdb=" CB VAL C 332 " ideal model delta harmonic sigma weight residual -122.00 -131.14 9.14 0 2.50e+00 1.60e-01 1.34e+01 dihedral pdb=" C VAL B 332 " pdb=" N VAL B 332 " pdb=" CA VAL B 332 " pdb=" CB VAL B 332 " ideal model delta harmonic sigma weight residual -122.00 -131.14 9.14 0 2.50e+00 1.60e-01 1.34e+01 dihedral pdb=" C VAL A 332 " pdb=" N VAL A 332 " pdb=" CA VAL A 332 " pdb=" CB VAL A 332 " ideal model delta harmonic sigma weight residual -122.00 -131.14 9.14 0 2.50e+00 1.60e-01 1.34e+01 ... (remaining 9321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2059 0.067 - 0.133: 305 0.133 - 0.200: 49 0.200 - 0.267: 37 0.267 - 0.334: 10 Chirality restraints: 2460 Sorted by residual: chirality pdb=" CA ARG B 338 " pdb=" N ARG B 338 " pdb=" C ARG B 338 " pdb=" CB ARG B 338 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA ARG C 338 " pdb=" N ARG C 338 " pdb=" C ARG C 338 " pdb=" CB ARG C 338 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA ARG D 338 " pdb=" N ARG D 338 " pdb=" C ARG D 338 " pdb=" CB ARG D 338 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 2457 not shown) Planarity restraints: 2604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 57 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.61e+00 pdb=" C ARG D 57 " 0.051 2.00e-02 2.50e+03 pdb=" O ARG D 57 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA D 58 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 57 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.61e+00 pdb=" C ARG A 57 " -0.051 2.00e-02 2.50e+03 pdb=" O ARG A 57 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA A 58 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 57 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.56e+00 pdb=" C ARG C 57 " 0.051 2.00e-02 2.50e+03 pdb=" O ARG C 57 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA C 58 " -0.017 2.00e-02 2.50e+03 ... (remaining 2601 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 6313 2.91 - 3.40: 15536 3.40 - 3.90: 26971 3.90 - 4.40: 31081 4.40 - 4.90: 49867 Nonbonded interactions: 129768 Sorted by model distance: nonbonded pdb=" OH TYR A 109 " pdb=" OD1 ASP A 114 " model vdw 2.408 2.440 nonbonded pdb=" OH TYR B 109 " pdb=" OD1 ASP B 114 " model vdw 2.408 2.440 nonbonded pdb=" OH TYR D 109 " pdb=" OD1 ASP D 114 " model vdw 2.408 2.440 nonbonded pdb=" OH TYR C 109 " pdb=" OD1 ASP C 114 " model vdw 2.408 2.440 nonbonded pdb=" O TYR A 47 " pdb=" NZ LYS A 55 " model vdw 2.436 2.520 ... (remaining 129763 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 40 through 527 or resid 601)) selection = chain 'B' selection = (chain 'C' and (resid 40 through 527 or resid 601)) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.150 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: 5.970 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 44.180 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 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 : 0.007 0.120 15712 Z= 0.431 Angle : 0.812 10.700 21332 Z= 0.508 Chirality : 0.060 0.334 2460 Planarity : 0.005 0.044 2600 Dihedral : 16.321 89.861 5788 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 17.94 % Favored : 82.06 % 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: 1.57 (0.19), residues: 1844 helix: 1.57 (0.15), residues: 1116 sheet: 0.95 (0.31), residues: 252 loop : -0.02 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 491 HIS 0.007 0.002 HIS C 234 PHE 0.021 0.002 PHE A 474 TYR 0.014 0.002 TYR D 497 ARG 0.006 0.001 ARG D 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.762 Fit side-chains REVERT: C 303 VAL cc_start: 0.7753 (t) cc_final: 0.7550 (p) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 1.1672 time to fit residues: 253.0826 Evaluate side-chains 153 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 7.9990 chunk 139 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 167 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS A 327 GLN B 234 HIS C 234 HIS C 327 GLN D 234 HIS D 327 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15712 Z= 0.164 Angle : 0.509 6.138 21332 Z= 0.265 Chirality : 0.039 0.132 2460 Planarity : 0.004 0.035 2600 Dihedral : 6.479 54.577 2316 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 4.13 % Allowed : 14.23 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.19), residues: 1844 helix: 2.06 (0.15), residues: 1100 sheet: 1.16 (0.32), residues: 252 loop : 0.05 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 157 HIS 0.003 0.001 HIS D 486 PHE 0.016 0.002 PHE D 235 TYR 0.013 0.001 TYR D 497 ARG 0.003 0.000 ARG C 318 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 164 time to evaluate : 1.910 Fit side-chains REVERT: A 44 ARG cc_start: 0.5814 (OUTLIER) cc_final: 0.5101 (ptm160) REVERT: A 65 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7146 (mtmp) REVERT: A 95 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: B 44 ARG cc_start: 0.5813 (OUTLIER) cc_final: 0.5075 (ptm160) REVERT: B 65 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7132 (mtmp) REVERT: C 44 ARG cc_start: 0.5839 (OUTLIER) cc_final: 0.5101 (ptm160) REVERT: C 65 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.7114 (mtmp) REVERT: C 276 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7421 (mt-10) REVERT: D 44 ARG cc_start: 0.5838 (OUTLIER) cc_final: 0.5127 (ptm160) REVERT: D 65 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7187 (mtmp) outliers start: 69 outliers final: 16 residues processed: 197 average time/residue: 1.2945 time to fit residues: 281.2099 Evaluate side-chains 173 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 147 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 488 SER Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 64 CYS Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 488 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 113 optimal weight: 0.0270 chunk 46 optimal weight: 10.0000 chunk 167 optimal weight: 6.9990 chunk 180 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 chunk 165 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 overall best weight: 4.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN B 327 GLN C 327 GLN C 469 ASN D 327 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 15712 Z= 0.370 Angle : 0.617 6.253 21332 Z= 0.324 Chirality : 0.045 0.138 2460 Planarity : 0.005 0.039 2600 Dihedral : 6.666 54.345 2316 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.49 % Allowed : 12.86 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.19), residues: 1844 helix: 1.76 (0.15), residues: 1112 sheet: 1.24 (0.32), residues: 252 loop : -0.08 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 157 HIS 0.010 0.002 HIS B 486 PHE 0.021 0.003 PHE B 474 TYR 0.015 0.002 TYR D 497 ARG 0.006 0.001 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 139 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6084 (OUTLIER) cc_final: 0.5618 (mtm-85) REVERT: A 65 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7294 (mtmp) REVERT: A 276 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7459 (mt-10) REVERT: A 303 VAL cc_start: 0.7688 (t) cc_final: 0.7469 (p) REVERT: A 327 GLN cc_start: 0.5767 (OUTLIER) cc_final: 0.5539 (tm-30) REVERT: A 358 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7995 (mp) REVERT: B 44 ARG cc_start: 0.5988 (OUTLIER) cc_final: 0.5586 (mtm-85) REVERT: B 65 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7293 (mtmp) REVERT: B 276 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7457 (mt-10) REVERT: B 303 VAL cc_start: 0.7687 (t) cc_final: 0.7472 (p) REVERT: B 358 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8012 (mp) REVERT: C 44 ARG cc_start: 0.6012 (OUTLIER) cc_final: 0.5617 (mtm-85) REVERT: C 65 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7280 (mtmp) REVERT: C 276 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7465 (mt-10) REVERT: C 303 VAL cc_start: 0.7723 (t) cc_final: 0.7511 (p) REVERT: C 327 GLN cc_start: 0.5776 (OUTLIER) cc_final: 0.5555 (tm-30) REVERT: C 358 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8004 (mp) REVERT: D 44 ARG cc_start: 0.5974 (OUTLIER) cc_final: 0.5554 (mtm-85) REVERT: D 65 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7293 (mtmp) REVERT: D 115 ASP cc_start: 0.7369 (OUTLIER) cc_final: 0.7037 (m-30) REVERT: D 276 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7470 (mt-10) REVERT: D 303 VAL cc_start: 0.7692 (t) cc_final: 0.7474 (p) REVERT: D 327 GLN cc_start: 0.5771 (OUTLIER) cc_final: 0.5547 (tm-30) REVERT: D 358 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7978 (mp) outliers start: 75 outliers final: 32 residues processed: 191 average time/residue: 1.1969 time to fit residues: 253.7196 Evaluate side-chains 173 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 121 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 64 CYS Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 363 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 167 optimal weight: 0.9990 chunk 177 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 159 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN B 327 GLN C 327 GLN D 327 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15712 Z= 0.199 Angle : 0.521 6.076 21332 Z= 0.271 Chirality : 0.040 0.126 2460 Planarity : 0.004 0.037 2600 Dihedral : 6.491 53.425 2316 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.71 % Allowed : 13.04 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.19), residues: 1844 helix: 1.99 (0.15), residues: 1112 sheet: 1.30 (0.32), residues: 252 loop : -0.01 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 491 HIS 0.005 0.001 HIS D 486 PHE 0.014 0.002 PHE B 474 TYR 0.013 0.002 TYR A 497 ARG 0.004 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 144 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6160 (OUTLIER) cc_final: 0.5959 (ptm-80) REVERT: A 65 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7285 (mtmm) REVERT: A 95 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: A 115 ASP cc_start: 0.7354 (OUTLIER) cc_final: 0.7017 (m-30) REVERT: A 276 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7460 (mt-10) REVERT: A 327 GLN cc_start: 0.5657 (OUTLIER) cc_final: 0.5449 (tm-30) REVERT: A 358 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7970 (mp) REVERT: B 44 ARG cc_start: 0.6161 (OUTLIER) cc_final: 0.5433 (mtm-85) REVERT: B 65 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7278 (mtmm) REVERT: B 115 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.7007 (m-30) REVERT: B 276 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7461 (mt-10) REVERT: B 327 GLN cc_start: 0.5831 (OUTLIER) cc_final: 0.5601 (tm-30) REVERT: B 358 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7985 (mp) REVERT: C 44 ARG cc_start: 0.6151 (OUTLIER) cc_final: 0.5565 (mtm-85) REVERT: C 65 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7160 (ttmt) REVERT: C 115 ASP cc_start: 0.7354 (OUTLIER) cc_final: 0.7016 (m-30) REVERT: C 276 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7452 (mt-10) REVERT: C 327 GLN cc_start: 0.5651 (OUTLIER) cc_final: 0.5425 (tm-30) REVERT: C 358 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7985 (mp) REVERT: D 44 ARG cc_start: 0.6151 (OUTLIER) cc_final: 0.5573 (mtm-85) REVERT: D 65 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7175 (ttmt) REVERT: D 276 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7460 (mt-10) REVERT: D 327 GLN cc_start: 0.5665 (OUTLIER) cc_final: 0.5436 (tm-30) REVERT: D 358 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7959 (mp) outliers start: 62 outliers final: 27 residues processed: 182 average time/residue: 1.3532 time to fit residues: 270.9787 Evaluate side-chains 179 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 128 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 64 CYS Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 401 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.3980 chunk 100 optimal weight: 3.9990 chunk 2 optimal weight: 0.0050 chunk 132 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 159 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 overall best weight: 1.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN B 247 ASN B 327 GLN C 247 ASN C 327 GLN D 327 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15712 Z= 0.158 Angle : 0.500 6.763 21332 Z= 0.256 Chirality : 0.039 0.123 2460 Planarity : 0.004 0.035 2600 Dihedral : 6.354 53.333 2316 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.81 % Allowed : 14.17 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.19), residues: 1844 helix: 2.14 (0.15), residues: 1100 sheet: 1.33 (0.32), residues: 252 loop : 0.04 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 354 HIS 0.004 0.001 HIS B 486 PHE 0.012 0.001 PHE C 474 TYR 0.013 0.001 TYR C 497 ARG 0.002 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 138 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.5948 (OUTLIER) cc_final: 0.5339 (mtm-85) REVERT: A 65 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7194 (ttmt) REVERT: A 95 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: A 115 ASP cc_start: 0.7348 (m-30) cc_final: 0.7000 (m-30) REVERT: A 276 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7431 (mt-10) REVERT: A 358 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7938 (mp) REVERT: B 44 ARG cc_start: 0.5947 (OUTLIER) cc_final: 0.5333 (mtm-85) REVERT: B 65 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7193 (ttmt) REVERT: B 115 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.7001 (m-30) REVERT: B 276 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7426 (mt-10) REVERT: B 358 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7960 (mp) REVERT: C 44 ARG cc_start: 0.6095 (OUTLIER) cc_final: 0.5384 (mtm-85) REVERT: C 65 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7183 (ttmt) REVERT: C 115 ASP cc_start: 0.7347 (m-30) cc_final: 0.7001 (m-30) REVERT: C 276 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7429 (mt-10) REVERT: C 358 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7924 (mp) REVERT: D 44 ARG cc_start: 0.6101 (OUTLIER) cc_final: 0.5502 (mtm-85) REVERT: D 65 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7187 (ttmt) REVERT: D 276 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7431 (mt-10) REVERT: D 358 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7900 (mp) outliers start: 47 outliers final: 17 residues processed: 175 average time/residue: 1.2530 time to fit residues: 242.3792 Evaluate side-chains 163 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 128 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 358 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN B 247 ASN B 327 GLN C 247 ASN C 327 GLN D 327 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15712 Z= 0.310 Angle : 0.584 6.334 21332 Z= 0.305 Chirality : 0.043 0.131 2460 Planarity : 0.004 0.048 2600 Dihedral : 6.539 53.990 2316 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.67 % Allowed : 12.44 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.99 (0.19), residues: 1844 helix: 1.91 (0.15), residues: 1116 sheet: 1.28 (0.32), residues: 252 loop : 0.01 (0.31), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 491 HIS 0.008 0.002 HIS B 486 PHE 0.019 0.002 PHE D 474 TYR 0.015 0.002 TYR D 497 ARG 0.004 0.001 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 138 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.5912 (OUTLIER) cc_final: 0.5356 (mtm-85) REVERT: A 65 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7286 (mtmp) REVERT: A 95 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: A 276 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7479 (mt-10) REVERT: A 358 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7962 (mp) REVERT: B 44 ARG cc_start: 0.5892 (OUTLIER) cc_final: 0.5322 (mtm-85) REVERT: B 65 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7278 (mtmp) REVERT: B 115 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.6997 (m-30) REVERT: B 276 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7473 (mt-10) REVERT: B 358 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7993 (mp) REVERT: C 44 ARG cc_start: 0.5950 (OUTLIER) cc_final: 0.5378 (ptm160) REVERT: C 65 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7270 (mtmp) REVERT: C 276 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7471 (mt-10) REVERT: C 303 VAL cc_start: 0.7709 (t) cc_final: 0.7500 (p) REVERT: C 358 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7995 (mp) REVERT: D 65 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7283 (mtmp) REVERT: D 115 ASP cc_start: 0.7359 (OUTLIER) cc_final: 0.7023 (m-30) REVERT: D 276 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7465 (mt-10) REVERT: D 358 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7963 (mp) outliers start: 78 outliers final: 34 residues processed: 194 average time/residue: 1.2805 time to fit residues: 275.6103 Evaluate side-chains 178 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 126 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain D residue 64 CYS Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 401 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 177 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 108 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN A 327 GLN B 247 ASN B 327 GLN C 247 ASN C 327 GLN D 247 ASN D 327 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15712 Z= 0.174 Angle : 0.507 6.057 21332 Z= 0.263 Chirality : 0.039 0.125 2460 Planarity : 0.004 0.063 2600 Dihedral : 6.379 53.182 2316 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.29 % Allowed : 13.88 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.19), residues: 1844 helix: 2.15 (0.15), residues: 1104 sheet: 1.35 (0.32), residues: 252 loop : 0.05 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 491 HIS 0.004 0.001 HIS A 486 PHE 0.022 0.002 PHE D 333 TYR 0.012 0.001 TYR A 497 ARG 0.009 0.000 ARG D 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 131 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.5967 (OUTLIER) cc_final: 0.5368 (mtm-85) REVERT: A 65 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.7143 (ttmt) REVERT: A 95 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7093 (mp0) REVERT: A 115 ASP cc_start: 0.7343 (m-30) cc_final: 0.6993 (m-30) REVERT: A 276 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7440 (mt-10) REVERT: A 358 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7948 (mp) REVERT: B 44 ARG cc_start: 0.5910 (OUTLIER) cc_final: 0.5314 (mtm-85) REVERT: B 65 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.7100 (ttmt) REVERT: B 115 ASP cc_start: 0.7344 (OUTLIER) cc_final: 0.6998 (m-30) REVERT: B 276 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7460 (mt-10) REVERT: B 358 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7955 (mp) REVERT: C 44 ARG cc_start: 0.5823 (OUTLIER) cc_final: 0.5220 (mtm-85) REVERT: C 65 LYS cc_start: 0.7587 (OUTLIER) cc_final: 0.7195 (ttmt) REVERT: C 95 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: C 276 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7425 (mt-10) REVERT: C 358 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7963 (mp) REVERT: D 44 ARG cc_start: 0.5911 (ptm160) cc_final: 0.5413 (mtm-85) REVERT: D 65 LYS cc_start: 0.7540 (OUTLIER) cc_final: 0.7094 (ttmt) REVERT: D 115 ASP cc_start: 0.7309 (OUTLIER) cc_final: 0.6976 (m-30) REVERT: D 276 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7442 (mt-10) REVERT: D 358 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7971 (mp) outliers start: 55 outliers final: 23 residues processed: 182 average time/residue: 1.1753 time to fit residues: 238.4342 Evaluate side-chains 167 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 125 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 401 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 161 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN A 327 GLN B 247 ASN B 327 GLN C 247 ASN C 327 GLN D 247 ASN D 327 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 15712 Z= 0.316 Angle : 0.590 6.192 21332 Z= 0.309 Chirality : 0.043 0.131 2460 Planarity : 0.005 0.047 2600 Dihedral : 6.559 54.070 2316 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.71 % Allowed : 13.70 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.19), residues: 1844 helix: 1.90 (0.15), residues: 1116 sheet: 1.33 (0.32), residues: 252 loop : 0.03 (0.31), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 491 HIS 0.009 0.002 HIS D 486 PHE 0.026 0.002 PHE D 333 TYR 0.015 0.002 TYR C 497 ARG 0.005 0.001 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 139 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.5926 (OUTLIER) cc_final: 0.5369 (mtm-85) REVERT: A 65 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7276 (mtmp) REVERT: A 95 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: A 276 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7464 (mt-10) REVERT: A 358 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7970 (mp) REVERT: B 44 ARG cc_start: 0.5954 (OUTLIER) cc_final: 0.5369 (mtm-85) REVERT: B 65 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7280 (mtmp) REVERT: B 276 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7475 (mt-10) REVERT: B 358 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7996 (mp) REVERT: C 44 ARG cc_start: 0.5967 (OUTLIER) cc_final: 0.5378 (mtm-85) REVERT: C 65 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7299 (mtmp) REVERT: C 276 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7471 (mt-10) REVERT: C 303 VAL cc_start: 0.7693 (t) cc_final: 0.7480 (p) REVERT: C 358 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7993 (mp) REVERT: D 65 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7275 (mtmp) REVERT: D 115 ASP cc_start: 0.7333 (OUTLIER) cc_final: 0.6994 (m-30) REVERT: D 276 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7464 (mt-10) REVERT: D 358 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7964 (mp) outliers start: 62 outliers final: 32 residues processed: 188 average time/residue: 1.1949 time to fit residues: 249.1545 Evaluate side-chains 183 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 134 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 65 LYS Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 318 ARG Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 401 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 chunk 165 optimal weight: 20.0000 chunk 99 optimal weight: 0.1980 chunk 71 optimal weight: 7.9990 chunk 129 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 149 optimal weight: 0.5980 chunk 156 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 GLN A 469 ASN B 469 ASN C 327 GLN D 469 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15712 Z= 0.138 Angle : 0.487 6.153 21332 Z= 0.249 Chirality : 0.038 0.128 2460 Planarity : 0.004 0.049 2600 Dihedral : 6.317 53.110 2316 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.45 % Allowed : 15.13 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.20), residues: 1844 helix: 2.26 (0.15), residues: 1104 sheet: 1.34 (0.32), residues: 252 loop : 0.10 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 354 HIS 0.003 0.001 HIS A 234 PHE 0.024 0.001 PHE D 333 TYR 0.012 0.001 TYR D 497 ARG 0.006 0.000 ARG D 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 127 time to evaluate : 1.856 Fit side-chains REVERT: A 44 ARG cc_start: 0.5789 (OUTLIER) cc_final: 0.5296 (mtm-85) REVERT: A 276 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7401 (mt-10) REVERT: B 44 ARG cc_start: 0.5714 (OUTLIER) cc_final: 0.5205 (mtm-85) REVERT: B 95 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: B 276 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7400 (mt-10) REVERT: C 44 ARG cc_start: 0.5737 (OUTLIER) cc_final: 0.5235 (mtm-85) REVERT: C 95 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7055 (mp0) REVERT: C 276 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7396 (mt-10) REVERT: D 44 ARG cc_start: 0.5893 (OUTLIER) cc_final: 0.5293 (mtm-85) REVERT: D 95 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: D 276 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7398 (mt-10) outliers start: 41 outliers final: 15 residues processed: 166 average time/residue: 1.0488 time to fit residues: 196.4262 Evaluate side-chains 154 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 128 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 401 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 82 optimal weight: 6.9990 chunk 121 optimal weight: 0.9990 chunk 183 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 15712 Z= 0.394 Angle : 0.630 7.315 21332 Z= 0.331 Chirality : 0.046 0.135 2460 Planarity : 0.005 0.037 2600 Dihedral : 6.589 54.205 2316 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.45 % Allowed : 15.13 % Favored : 82.42 % 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: 1.91 (0.19), residues: 1844 helix: 1.82 (0.15), residues: 1116 sheet: 1.31 (0.32), residues: 252 loop : 0.02 (0.31), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 491 HIS 0.010 0.002 HIS B 486 PHE 0.022 0.003 PHE D 474 TYR 0.015 0.003 TYR D 404 ARG 0.006 0.001 ARG C 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 145 time to evaluate : 1.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.5878 (OUTLIER) cc_final: 0.5318 (mtm-85) REVERT: A 276 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7469 (mt-10) REVERT: A 303 VAL cc_start: 0.7676 (t) cc_final: 0.7452 (p) REVERT: B 44 ARG cc_start: 0.5955 (OUTLIER) cc_final: 0.5381 (mtm-85) REVERT: B 65 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7243 (mtmp) REVERT: B 276 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7467 (mt-10) REVERT: B 303 VAL cc_start: 0.7674 (t) cc_final: 0.7450 (p) REVERT: C 44 ARG cc_start: 0.5968 (OUTLIER) cc_final: 0.5390 (mtm-85) REVERT: C 276 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7464 (mt-10) REVERT: C 303 VAL cc_start: 0.7705 (t) cc_final: 0.7493 (p) REVERT: D 44 ARG cc_start: 0.5823 (OUTLIER) cc_final: 0.5086 (ptm160) REVERT: D 276 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7472 (mt-10) REVERT: D 303 VAL cc_start: 0.7666 (t) cc_final: 0.7440 (p) outliers start: 41 outliers final: 24 residues processed: 179 average time/residue: 1.2846 time to fit residues: 254.5409 Evaluate side-chains 170 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 137 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 69 GLN Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 64 CYS Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain D residue 44 ARG Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 318 ARG Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 401 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 21 optimal weight: 0.1980 chunk 40 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 61 optimal weight: 0.0570 chunk 150 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.138876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.093863 restraints weight = 15654.496| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.45 r_work: 0.2903 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15712 Z= 0.156 Angle : 0.499 6.094 21332 Z= 0.255 Chirality : 0.039 0.125 2460 Planarity : 0.004 0.048 2600 Dihedral : 6.352 52.986 2316 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.73 % Allowed : 15.67 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.19), residues: 1844 helix: 2.21 (0.15), residues: 1104 sheet: 1.33 (0.32), residues: 252 loop : 0.08 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 354 HIS 0.003 0.001 HIS D 234 PHE 0.020 0.001 PHE D 333 TYR 0.013 0.001 TYR D 497 ARG 0.006 0.000 ARG D 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5018.11 seconds wall clock time: 89 minutes 46.27 seconds (5386.27 seconds total)