Starting phenix.real_space_refine on Thu Nov 16 12:58:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq6_25377/11_2023/7sq6_25377_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq6_25377/11_2023/7sq6_25377.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq6_25377/11_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_25377/11_2023/7sq6_25377_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq6_25377/11_2023/7sq6_25377_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq6_25377/11_2023/7sq6_25377.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq6_25377/11_2023/7sq6_25377.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq6_25377/11_2023/7sq6_25377_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq6_25377/11_2023/7sq6_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-1.21rc1-5144/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: 8.22, per 1000 atoms: 0.54 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: 5.40 Conformation dependent library (CDL) restraints added in 2.5 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: 2.87 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: 4.68 Time building geometry restraints manager: 5.92 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: 556 49.93 - 74.90: 68 74.90 - 99.87: 28 99.87 - 124.83: 4 Dihedral angle restraints: 9092 sinusoidal: 3608 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 9089 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: 0.950 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: 5.850 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 40.680 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.120 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:13.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.190 ------------------------------------------------------------------------------- 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 : 16.722 124.834 5556 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 *********************** 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 : 1.861 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 1.0867 time to fit residues: 235.5469 Evaluate side-chains 152 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.558 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1699 ------------------------------------------------------------------------------- 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 B 327 GLN C 234 HIS C 327 GLN D 234 HIS D 327 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.0958 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= 0.163 Angle : 0.524 7.702 21332 Z= 0.268 Chirality : 0.039 0.134 2460 Planarity : 0.004 0.035 2600 Dihedral : 7.908 121.617 2084 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 4.43 % Allowed : 14.00 % Favored : 81.58 % 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: 1.17 (0.32), residues: 252 loop : 0.06 (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 241 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 167 time to evaluate : 1.813 Fit side-chains outliers start: 74 outliers final: 16 residues processed: 203 average time/residue: 1.3165 time to fit residues: 295.3244 Evaluate side-chains 165 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 149 time to evaluate : 1.718 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 4 average time/residue: 0.1335 time to fit residues: 3.4279 ------------------------------------------------------------------------------- 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: 4.9990 chunk 113 optimal weight: 0.4980 chunk 46 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- 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 B 469 ASN C 327 GLN D 327 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 15712 Z= 0.400 Angle : 0.654 7.182 21332 Z= 0.338 Chirality : 0.046 0.141 2460 Planarity : 0.005 0.040 2600 Dihedral : 8.296 124.114 2084 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.31 % Allowed : 12.80 % 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: 1.74 (0.19), residues: 1844 helix: 1.69 (0.15), residues: 1116 sheet: 1.25 (0.33), residues: 252 loop : -0.08 (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 213 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 141 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 32 residues processed: 196 average time/residue: 1.2286 time to fit residues: 267.3938 Evaluate side-chains 156 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 124 time to evaluate : 1.706 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 32 residues processed: 0 time to fit residues: 2.3048 ------------------------------------------------------------------------------- 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: 2.9990 chunk 125 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 112 optimal weight: 0.8980 chunk 167 optimal weight: 0.8980 chunk 177 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 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 327 GLN C 327 GLN D 327 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15712 Z= 0.171 Angle : 0.528 8.218 21332 Z= 0.268 Chirality : 0.039 0.124 2460 Planarity : 0.004 0.037 2600 Dihedral : 7.868 121.272 2084 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.65 % Allowed : 13.10 % 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: 2.16 (0.19), residues: 1844 helix: 2.09 (0.15), residues: 1100 sheet: 1.37 (0.32), residues: 252 loop : -0.00 (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 197 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 136 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 34 residues processed: 185 average time/residue: 1.2571 time to fit residues: 261.3308 Evaluate side-chains 160 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 126 time to evaluate : 1.847 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 34 residues processed: 0 time to fit residues: 2.3401 ------------------------------------------------------------------------------- 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: 9.9990 chunk 132 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 151 optimal weight: 0.0270 chunk 122 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 chunk 159 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 overall best weight: 1.3642 ------------------------------------------------------------------------------- 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 327 GLN C 327 GLN D 327 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15712 Z= 0.161 Angle : 0.518 8.393 21332 Z= 0.263 Chirality : 0.039 0.123 2460 Planarity : 0.004 0.077 2600 Dihedral : 7.660 120.623 2084 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.47 % Allowed : 13.34 % Favored : 83.19 % 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: 2.33 (0.19), residues: 1844 helix: 2.24 (0.15), residues: 1100 sheet: 1.41 (0.32), residues: 252 loop : 0.06 (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 191 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 133 time to evaluate : 1.858 Fit side-chains outliers start: 58 outliers final: 32 residues processed: 187 average time/residue: 1.1231 time to fit residues: 235.7276 Evaluate side-chains 173 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 141 time to evaluate : 1.678 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 32 residues processed: 0 time to fit residues: 2.3028 ------------------------------------------------------------------------------- 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: 0.9980 chunk 160 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 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: 10.0000 chunk 93 optimal weight: 9.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15712 Z= 0.284 Angle : 0.587 8.251 21332 Z= 0.303 Chirality : 0.042 0.130 2460 Planarity : 0.005 0.053 2600 Dihedral : 7.848 122.585 2084 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.17 % Allowed : 14.17 % 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: 2.16 (0.19), residues: 1844 helix: 2.05 (0.15), residues: 1116 sheet: 1.38 (0.32), residues: 252 loop : 0.03 (0.31), residues: 476 *********************** 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 197 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 144 time to evaluate : 1.810 Fit side-chains outliers start: 53 outliers final: 34 residues processed: 188 average time/residue: 1.1296 time to fit residues: 238.0549 Evaluate side-chains 158 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 124 time to evaluate : 1.732 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 34 residues processed: 0 time to fit residues: 2.3127 ------------------------------------------------------------------------------- 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: 2.9990 chunk 101 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15712 Z= 0.257 Angle : 0.563 8.332 21332 Z= 0.290 Chirality : 0.041 0.127 2460 Planarity : 0.004 0.047 2600 Dihedral : 7.818 122.193 2084 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.35 % Allowed : 13.94 % Favored : 82.72 % 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: 2.14 (0.19), residues: 1844 helix: 2.04 (0.15), residues: 1116 sheet: 1.35 (0.32), residues: 252 loop : 0.04 (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 207 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 151 time to evaluate : 1.887 Fit side-chains outliers start: 56 outliers final: 30 residues processed: 195 average time/residue: 1.1647 time to fit residues: 255.1379 Evaluate side-chains 164 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 134 time to evaluate : 1.758 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 30 residues processed: 0 time to fit residues: 2.5787 ------------------------------------------------------------------------------- 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: 10.0000 chunk 70 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 120 optimal weight: 0.2980 chunk 87 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 overall best weight: 4.0588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 ASN D 247 ASN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 15712 Z= 0.333 Angle : 0.617 8.256 21332 Z= 0.319 Chirality : 0.044 0.131 2460 Planarity : 0.005 0.045 2600 Dihedral : 7.947 123.260 2084 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.23 % Allowed : 13.70 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.93 (0.19), residues: 1844 helix: 1.84 (0.15), residues: 1116 sheet: 1.35 (0.32), residues: 252 loop : -0.01 (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 179 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 125 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 43 residues processed: 173 average time/residue: 1.0627 time to fit residues: 207.9534 Evaluate side-chains 168 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 125 time to evaluate : 1.637 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 43 residues processed: 0 time to fit residues: 2.1520 ------------------------------------------------------------------------------- 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: 0.8980 chunk 155 optimal weight: 2.9990 chunk 165 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 129 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 chunk 156 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15712 Z= 0.183 Angle : 0.533 8.394 21332 Z= 0.271 Chirality : 0.039 0.125 2460 Planarity : 0.004 0.037 2600 Dihedral : 7.734 121.257 2084 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.87 % Allowed : 14.23 % 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: 2.23 (0.20), residues: 1844 helix: 2.12 (0.15), residues: 1116 sheet: 1.34 (0.32), residues: 252 loop : 0.08 (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 172 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 124 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 38 residues processed: 172 average time/residue: 1.1401 time to fit residues: 221.4778 Evaluate side-chains 167 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 129 time to evaluate : 1.861 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 38 residues processed: 0 time to fit residues: 2.3963 ------------------------------------------------------------------------------- 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: 4.9990 chunk 106 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 183 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 112 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 15712 Z= 0.304 Angle : 0.592 8.285 21332 Z= 0.307 Chirality : 0.043 0.129 2460 Planarity : 0.005 0.037 2600 Dihedral : 7.860 122.685 2084 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.51 % Allowed : 14.83 % 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: 2.04 (0.19), residues: 1844 helix: 1.94 (0.15), residues: 1116 sheet: 1.33 (0.32), residues: 252 loop : 0.02 (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 174 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 132 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 38 residues processed: 174 average time/residue: 1.1042 time to fit residues: 217.5917 Evaluate side-chains 166 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 128 time to evaluate : 1.769 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 38 residues processed: 0 time to fit residues: 2.4483 ------------------------------------------------------------------------------- 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: 4.9990 chunk 44 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 40 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 150 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 = 0.3616 r_free = 0.3616 target = 0.137286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.095631 restraints weight = 15548.042| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.74 r_work: 0.2809 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15712 Z= 0.218 Angle : 0.549 8.386 21332 Z= 0.282 Chirality : 0.040 0.125 2460 Planarity : 0.004 0.036 2600 Dihedral : 7.773 121.671 2084 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.51 % Allowed : 15.25 % Favored : 82.24 % 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: 2.15 (0.19), residues: 1844 helix: 2.05 (0.15), residues: 1116 sheet: 1.29 (0.32), residues: 252 loop : 0.06 (0.31), residues: 476 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4898.03 seconds wall clock time: 88 minutes 40.72 seconds (5320.72 seconds total)