Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 17:27:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq6_25377/04_2023/7sq6_25377_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq6_25377/04_2023/7sq6_25377.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq6_25377/04_2023/7sq6_25377_neut_trim_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq6_25377/04_2023/7sq6_25377_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq6_25377/04_2023/7sq6_25377_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq6_25377/04_2023/7sq6_25377.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq6_25377/04_2023/7sq6_25377.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq6_25377/04_2023/7sq6_25377_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq6_25377/04_2023/7sq6_25377_neut_trim_updated.pdb" } resolution = 2.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-1.21rc1-4938/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 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 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 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 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: 8.17, per 1000 atoms: 0.53 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: 6.27 Conformation dependent library (CDL) restraints added in 2.3 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: 1.50 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: 4.79 Time building geometry restraints manager: 6.82 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=" CA LEU B 422 " pdb=" C LEU B 422 " ideal model delta sigma weight residual 1.522 1.569 -0.047 1.29e-02 6.01e+03 1.32e+01 bond pdb=" CA LEU C 422 " pdb=" C LEU C 422 " ideal model delta sigma weight residual 1.522 1.569 -0.047 1.29e-02 6.01e+03 1.32e+01 bond pdb=" CA LEU D 422 " pdb=" C LEU D 422 " ideal model delta sigma weight residual 1.522 1.569 -0.047 1.29e-02 6.01e+03 1.32e+01 bond pdb=" CA LEU A 422 " pdb=" C LEU A 422 " ideal model delta sigma weight residual 1.522 1.568 -0.047 1.29e-02 6.01e+03 1.31e+01 bond pdb=" C LEU A 422 " pdb=" N PRO A 423 " ideal model delta sigma weight residual 1.335 1.380 -0.045 1.30e-02 5.92e+03 1.19e+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 - 24.97: 8436 24.97 - 49.93: 552 49.93 - 74.90: 64 74.90 - 99.87: 28 99.87 - 124.83: 4 Dihedral angle restraints: 9084 sinusoidal: 3600 harmonic: 5484 Sorted by residual: dihedral pdb=" N1 AQV C 601 " pdb=" C10 AQV C 601 " pdb=" C9 AQV C 601 " pdb=" N2 AQV C 601 " ideal model delta sinusoidal sigma weight residual 182.01 57.18 124.83 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" N1 AQV D 601 " pdb=" C10 AQV D 601 " pdb=" C9 AQV D 601 " pdb=" N2 AQV D 601 " ideal model delta sinusoidal sigma weight residual 182.01 57.18 124.83 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" N1 AQV B 601 " pdb=" C10 AQV B 601 " pdb=" C9 AQV B 601 " pdb=" N2 AQV B 601 " ideal model delta sinusoidal sigma weight residual 182.01 57.19 124.82 1 3.00e+01 1.11e-03 1.68e+01 ... (remaining 9081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2063 0.067 - 0.133: 305 0.133 - 0.200: 45 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: 1.170 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: 6.580 Check model and map are aligned: 0.230 Set scattering table: 0.120 Process input model: 40.990 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.100 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:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.100 ------------------------------------------------------------------------------- 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 : 0.006 0.047 15712 Z= 0.372 Angle : 0.775 7.120 21332 Z= 0.502 Chirality : 0.060 0.334 2460 Planarity : 0.005 0.044 2600 Dihedral : 16.589 124.834 5548 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 % 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 *********************** 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 : 1.803 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 1.1087 time to fit residues: 240.4946 Evaluate side-chains 152 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.887 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2910 ------------------------------------------------------------------------------- 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: 0.8556 moved from start: 0.0868 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= 0.164 Angle : 0.525 7.479 21332 Z= 0.269 Chirality : 0.039 0.135 2460 Planarity : 0.004 0.036 2600 Dihedral : 7.399 122.335 2076 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer Outliers : 3.89 % 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: 2.07 (0.19), residues: 1844 helix: 2.04 (0.15), residues: 1100 sheet: 1.12 (0.31), residues: 252 loop : 0.04 (0.30), residues: 492 *********************** 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 228 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 163 time to evaluate : 1.940 Fit side-chains outliers start: 65 outliers final: 12 residues processed: 194 average time/residue: 1.3206 time to fit residues: 283.5043 Evaluate side-chains 168 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 156 time to evaluate : 1.825 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 4 average time/residue: 0.1330 time to fit residues: 3.4220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 139 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 167 optimal weight: 6.9990 chunk 180 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 165 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 286 HIS C 327 GLN D 286 HIS D 327 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.069 15712 Z= 0.469 Angle : 0.702 7.255 21332 Z= 0.365 Chirality : 0.049 0.146 2460 Planarity : 0.005 0.042 2600 Dihedral : 7.955 124.653 2076 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer Outliers : 3.65 % 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: 1.55 (0.15), residues: 1116 sheet: 1.18 (0.32), residues: 252 loop : -0.15 (0.30), residues: 476 *********************** 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 196 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 135 time to evaluate : 2.006 Fit side-chains outliers start: 61 outliers final: 28 residues processed: 183 average time/residue: 1.2452 time to fit residues: 253.9926 Evaluate side-chains 139 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 111 time to evaluate : 1.871 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 28 residues processed: 0 time to fit residues: 2.3629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 0.9990 chunk 125 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 112 optimal weight: 0.9990 chunk 167 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- 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 247 ASN C 327 GLN D 247 ASN D 327 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1204 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= 0.160 Angle : 0.525 7.277 21332 Z= 0.266 Chirality : 0.039 0.124 2460 Planarity : 0.004 0.049 2600 Dihedral : 7.541 121.720 2076 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer Outliers : 3.23 % 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: 2.17 (0.19), residues: 1844 helix: 2.10 (0.15), residues: 1100 sheet: 1.30 (0.32), residues: 252 loop : 0.04 (0.30), residues: 492 *********************** 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 181 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 127 time to evaluate : 1.842 Fit side-chains outliers start: 54 outliers final: 28 residues processed: 175 average time/residue: 1.0868 time to fit residues: 215.3967 Evaluate side-chains 152 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 124 time to evaluate : 1.802 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 28 residues processed: 0 time to fit residues: 2.4074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 151 optimal weight: 0.0030 chunk 122 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 159 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- 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 247 ASN C 286 HIS C 327 GLN D 247 ASN D 286 HIS D 327 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 15712 Z= 0.152 Angle : 0.515 8.452 21332 Z= 0.259 Chirality : 0.038 0.124 2460 Planarity : 0.004 0.036 2600 Dihedral : 7.356 120.893 2076 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer Outliers : 3.23 % 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: 2.34 (0.19), residues: 1844 helix: 2.26 (0.15), residues: 1100 sheet: 1.32 (0.32), residues: 252 loop : 0.07 (0.30), residues: 492 *********************** 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 200 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 146 time to evaluate : 1.853 Fit side-chains outliers start: 54 outliers final: 32 residues processed: 195 average time/residue: 1.1663 time to fit residues: 255.3766 Evaluate side-chains 173 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 141 time to evaluate : 1.886 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 32 residues processed: 0 time to fit residues: 2.5847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 178 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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** B 327 GLN C 247 ASN C 286 HIS ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN D 286 HIS D 327 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 15712 Z= 0.248 Angle : 0.561 7.327 21332 Z= 0.289 Chirality : 0.041 0.126 2460 Planarity : 0.004 0.067 2600 Dihedral : 7.522 122.397 2076 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 3.53 % 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: 2.13 (0.15), residues: 1112 sheet: 1.31 (0.32), residues: 252 loop : 0.07 (0.31), residues: 480 *********************** 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 200 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 141 time to evaluate : 1.904 Fit side-chains revert: symmetry clash outliers start: 59 outliers final: 32 residues processed: 191 average time/residue: 1.1400 time to fit residues: 244.0345 Evaluate side-chains 156 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 124 time to evaluate : 1.871 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 32 residues processed: 0 time to fit residues: 2.6580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 101 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 177 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 286 HIS ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN D 286 HIS D 327 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 15712 Z= 0.288 Angle : 0.583 6.914 21332 Z= 0.301 Chirality : 0.042 0.130 2460 Planarity : 0.005 0.077 2600 Dihedral : 7.694 123.308 2076 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 3.77 % 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: 2.09 (0.19), residues: 1844 helix: 1.99 (0.15), residues: 1116 sheet: 1.31 (0.32), residues: 252 loop : 0.05 (0.31), residues: 476 *********************** 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 200 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 137 time to evaluate : 1.861 Fit side-chains revert: symmetry clash outliers start: 63 outliers final: 32 residues processed: 185 average time/residue: 1.1399 time to fit residues: 238.5636 Evaluate side-chains 156 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 124 time to evaluate : 1.877 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 32 residues processed: 0 time to fit residues: 2.5627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 105 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 161 optimal weight: 0.6980 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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** B 247 ASN B 327 GLN C 286 HIS ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 HIS D 327 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 15712 Z= 0.204 Angle : 0.537 7.139 21332 Z= 0.274 Chirality : 0.040 0.123 2460 Planarity : 0.004 0.057 2600 Dihedral : 7.580 122.296 2076 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer Outliers : 2.51 % 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: 2.22 (0.19), residues: 1844 helix: 2.12 (0.15), residues: 1116 sheet: 1.29 (0.32), residues: 252 loop : 0.09 (0.31), residues: 476 *********************** 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 167 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 125 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 34 residues processed: 167 average time/residue: 0.9918 time to fit residues: 190.0044 Evaluate side-chains 164 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 130 time to evaluate : 1.834 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 34 residues processed: 0 time to fit residues: 2.3884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 0.0010 chunk 155 optimal weight: 7.9990 chunk 165 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 chunk 156 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 overall best weight: 2.3792 ------------------------------------------------------------------------------- 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 286 HIS ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 15712 Z= 0.224 Angle : 0.547 7.055 21332 Z= 0.281 Chirality : 0.040 0.124 2460 Planarity : 0.004 0.050 2600 Dihedral : 7.594 122.458 2076 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer Outliers : 2.75 % 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: 2.19 (0.19), residues: 1844 helix: 2.08 (0.15), residues: 1116 sheet: 1.31 (0.32), residues: 252 loop : 0.09 (0.31), residues: 476 *********************** 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 176 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 130 time to evaluate : 2.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 35 residues processed: 175 average time/residue: 1.0217 time to fit residues: 204.3630 Evaluate side-chains 160 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 125 time to evaluate : 1.827 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 35 residues processed: 0 time to fit residues: 2.4486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 82 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 183 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 112 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- 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 286 HIS ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 15712 Z= 0.265 Angle : 0.577 6.979 21332 Z= 0.296 Chirality : 0.042 0.140 2460 Planarity : 0.004 0.050 2600 Dihedral : 7.703 123.103 2076 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.08 (0.19), residues: 1844 helix: 1.98 (0.15), residues: 1116 sheet: 1.28 (0.32), residues: 252 loop : 0.06 (0.31), residues: 476 ********************** 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 164 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 125 time to evaluate : 1.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 37 residues processed: 164 average time/residue: 1.0768 time to fit residues: 201.3858 Evaluate side-chains 158 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 121 time to evaluate : 1.827 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 37 residues processed: 0 time to fit residues: 2.4761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 146 optimal weight: 0.0040 chunk 61 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 overall best weight: 1.7596 ------------------------------------------------------------------------------- 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 286 HIS ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.137971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.092781 restraints weight = 15553.324| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.44 r_work: 0.2884 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 15712 Z= 0.189 Angle : 0.532 7.174 21332 Z= 0.270 Chirality : 0.040 0.123 2460 Planarity : 0.004 0.046 2600 Dihedral : 7.559 122.102 2076 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer Outliers : 2.57 % 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: 2.19 (0.19), residues: 1844 helix: 2.11 (0.15), residues: 1104 sheet: 1.32 (0.32), residues: 252 loop : 0.07 (0.30), residues: 488 =============================================================================== Job complete usr+sys time: 4760.31 seconds wall clock time: 86 minutes 11.24 seconds (5171.24 seconds total)