Starting phenix.real_space_refine (version: 1.21rc1) on Sun Jul 9 09:49:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8act_15353/07_2023/8act_15353_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8act_15353/07_2023/8act_15353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8act_15353/07_2023/8act_15353.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8act_15353/07_2023/8act_15353.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8act_15353/07_2023/8act_15353_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8act_15353/07_2023/8act_15353_updated.pdb" } resolution = 3.6 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= 0.024 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 111 5.16 5 C 11989 2.51 5 N 3188 2.21 5 O 3547 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 262": "OD1" <-> "OD2" Residue "A TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 167": "OD1" <-> "OD2" Residue "D PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 18843 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7080 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 873, 7071 Classifications: {'peptide': 873} Link IDs: {'PTRANS': 31, 'TRANS': 841} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'M3L:plan-1': 2} Unresolved non-hydrogen planarities: 2 Conformer: "B" Number of residues, atoms: 873, 7071 Classifications: {'peptide': 873} Link IDs: {'PTRANS': 31, 'TRANS': 841} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'M3L:plan-1': 2} Unresolved non-hydrogen planarities: 2 bond proxies already assigned to first conformer: 7203 Chain: "B" Number of atoms: 6956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 857, 6956 Classifications: {'peptide': 857} Link IDs: {'PTRANS': 31, 'TRANS': 825} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'M3L:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1248 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "D" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1248 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "E" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1118 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 6, 'TRANS': 131} Chain breaks: 2 Chain: "F" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1127 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLN A 163 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 163 " occ=0.50 Time building chain proxies: 12.76, per 1000 atoms: 0.68 Number of scatterers: 18843 At special positions: 0 Unit cell: (94.08, 165.48, 182.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 111 16.00 P 6 15.00 Mg 2 11.99 O 3547 8.00 N 3188 7.00 C 11989 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 Time building additional restraints: 8.36 Conformation dependent library (CDL) restraints added in 3.6 seconds 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4378 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 105 helices and 14 sheets defined 52.7% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 Proline residue: A 14 - end of helix Processing helix chain 'A' and resid 20 through 27 Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 98 through 110 Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 154 through 168 Processing helix chain 'A' and resid 184 through 201 Processing helix chain 'A' and resid 216 through 230 removed outlier: 4.342A pdb=" N ASN A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Proline residue: A 225 - end of helix removed outlier: 3.755A pdb=" N PHE A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 273 Processing helix chain 'A' and resid 284 through 290 removed outlier: 3.531A pdb=" N ILE A 289 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 290 " --> pdb=" O PHE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 325 through 338 Processing helix chain 'A' and resid 343 through 361 removed outlier: 3.960A pdb=" N GLY A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASN A 361 " --> pdb=" O MET A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 388 Processing helix chain 'A' and resid 392 through 400 Processing helix chain 'A' and resid 417 through 447 Processing helix chain 'A' and resid 476 through 493 Processing helix chain 'A' and resid 495 through 503 removed outlier: 4.168A pdb=" N LYS A 502 " --> pdb=" O GLN A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 524 Processing helix chain 'A' and resid 530 through 539 removed outlier: 3.903A pdb=" N MET A 539 " --> pdb=" O GLU A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 555 Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 593 through 598 Processing helix chain 'A' and resid 603 through 611 Processing helix chain 'A' and resid 615 through 620 Processing helix chain 'A' and resid 647 through 664 removed outlier: 3.526A pdb=" N SER A 664 " --> pdb=" O THR A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 700 through 706 removed outlier: 4.148A pdb=" N ILE A 704 " --> pdb=" O GLU A 700 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N CYS A 705 " --> pdb=" O GLY A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 721 Processing helix chain 'A' and resid 723 through 725 No H-bonds generated for 'chain 'A' and resid 723 through 725' Processing helix chain 'A' and resid 738 through 747 Processing helix chain 'A' and resid 767 through 824 removed outlier: 4.482A pdb=" N LEU A 770 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 781 " --> pdb=" O ASP A 778 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 793 " --> pdb=" O ALA A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 839 Proline residue: A 838 - end of helix Processing helix chain 'A' and resid 842 through 905 Processing helix chain 'B' and resid 4 through 12 removed outlier: 6.602A pdb=" N ALA B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ALA B 12 " --> pdb=" O VAL B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 27 Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 98 through 110 removed outlier: 3.614A pdb=" N LEU B 102 " --> pdb=" O GLU B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'B' and resid 154 through 167 Processing helix chain 'B' and resid 184 through 197 Processing helix chain 'B' and resid 217 through 231 removed outlier: 3.864A pdb=" N ASN B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Proline residue: B 225 - end of helix removed outlier: 3.926A pdb=" N PHE B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 274 removed outlier: 3.664A pdb=" N VAL B 273 " --> pdb=" O LYS B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 291 removed outlier: 4.120A pdb=" N LEU B 290 " --> pdb=" O PHE B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 301 Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 325 through 339 Processing helix chain 'B' and resid 343 through 360 removed outlier: 3.828A pdb=" N MET B 357 " --> pdb=" O THR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 388 Processing helix chain 'B' and resid 392 through 400 Processing helix chain 'B' and resid 417 through 447 removed outlier: 4.049A pdb=" N ILE B 421 " --> pdb=" O VAL B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 493 Processing helix chain 'B' and resid 495 through 503 Processing helix chain 'B' and resid 518 through 524 removed outlier: 4.019A pdb=" N ILE B 524 " --> pdb=" O CYS B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 539 Processing helix chain 'B' and resid 547 through 551 Processing helix chain 'B' and resid 553 through 556 No H-bonds generated for 'chain 'B' and resid 553 through 556' Processing helix chain 'B' and resid 593 through 598 Processing helix chain 'B' and resid 603 through 610 Processing helix chain 'B' and resid 615 through 623 removed outlier: 3.557A pdb=" N ALA B 622 " --> pdb=" O SER B 618 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASN B 623 " --> pdb=" O THR B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 664 removed outlier: 3.744A pdb=" N SER B 664 " --> pdb=" O THR B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 696 Processing helix chain 'B' and resid 698 through 707 Processing helix chain 'B' and resid 715 through 722 Processing helix chain 'B' and resid 739 through 747 Processing helix chain 'B' and resid 769 through 825 Processing helix chain 'B' and resid 828 through 834 removed outlier: 4.045A pdb=" N LEU B 832 " --> pdb=" O PRO B 828 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR B 833 " --> pdb=" O TRP B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 897 Processing helix chain 'C' and resid 48 through 61 Processing helix chain 'C' and resid 76 through 82 Processing helix chain 'C' and resid 89 through 96 removed outlier: 4.133A pdb=" N LEU C 96 " --> pdb=" O VAL C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 105 Processing helix chain 'C' and resid 111 through 124 Proline residue: C 116 - end of helix Processing helix chain 'C' and resid 130 through 138 Processing helix chain 'C' and resid 150 through 158 Processing helix chain 'C' and resid 166 through 172 Processing helix chain 'C' and resid 185 through 194 Processing helix chain 'D' and resid 48 through 61 Processing helix chain 'D' and resid 73 through 82 removed outlier: 4.195A pdb=" N GLY D 77 " --> pdb=" O TYR D 73 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASP D 78 " --> pdb=" O GLY D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 95 Processing helix chain 'D' and resid 101 through 106 Processing helix chain 'D' and resid 111 through 124 Proline residue: D 116 - end of helix Processing helix chain 'D' and resid 130 through 138 Processing helix chain 'D' and resid 150 through 159 Processing helix chain 'D' and resid 166 through 172 Processing helix chain 'D' and resid 185 through 194 Processing helix chain 'E' and resid 29 through 36 Processing helix chain 'E' and resid 47 through 55 removed outlier: 3.732A pdb=" N ARG E 50 " --> pdb=" O ASN E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 72 removed outlier: 4.659A pdb=" N MET E 69 " --> pdb=" O GLU E 65 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ILE E 70 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS E 71 " --> pdb=" O ASP E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 90 removed outlier: 4.422A pdb=" N LYS E 89 " --> pdb=" O MET E 85 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU E 90 " --> pdb=" O PHE E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 106 Processing helix chain 'E' and resid 116 through 126 Processing helix chain 'E' and resid 132 through 141 removed outlier: 4.190A pdb=" N GLN E 137 " --> pdb=" O GLU E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 159 Processing helix chain 'F' and resid 23 through 36 Processing helix chain 'F' and resid 46 through 56 Processing helix chain 'F' and resid 65 through 72 Processing helix chain 'F' and resid 79 through 89 Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 116 through 123 Processing helix chain 'F' and resid 132 through 138 Processing helix chain 'F' and resid 152 through 161 removed outlier: 3.680A pdb=" N ILE F 159 " --> pdb=" O LEU F 155 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 36 through 40 removed outlier: 6.866A pdb=" N THR A 60 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG A 54 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LYS A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL A 59 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL A 71 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 115 through 118 Processing sheet with id= C, first strand: chain 'A' and resid 401 through 406 Processing sheet with id= D, first strand: chain 'A' and resid 563 through 565 Processing sheet with id= E, first strand: chain 'A' and resid 757 through 759 Processing sheet with id= F, first strand: chain 'A' and resid 363 through 366 removed outlier: 4.743A pdb=" N LYS A 363 " --> pdb=" O GLY A 377 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY A 377 " --> pdb=" O LYS A 363 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LYS A 365 " --> pdb=" O PRO A 375 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 37 through 40 Processing sheet with id= H, first strand: chain 'B' and resid 53 through 55 removed outlier: 3.730A pdb=" N SER B 53 " --> pdb=" O THR B 60 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 115 through 118 removed outlier: 3.889A pdb=" N PHE B 121 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 173 " --> pdb=" O HIS B 666 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN B 172 " --> pdb=" O PHE B 456 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 363 through 366 removed outlier: 4.424A pdb=" N LYS B 363 " --> pdb=" O ASP B 376 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP B 376 " --> pdb=" O LYS B 363 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 577 through 581 removed outlier: 3.775A pdb=" N PHE B 577 " --> pdb=" O TYR B 588 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 711 through 714 removed outlier: 3.586A pdb=" N ASN B 711 " --> pdb=" O PHE B 765 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 70 through 72 Processing sheet with id= N, first strand: chain 'D' and resid 147 through 149 877 hydrogen bonds defined for protein. 2389 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: 6.29 Time building geometry restraints manager: 8.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6183 1.34 - 1.46: 4054 1.46 - 1.58: 8763 1.58 - 1.70: 6 1.70 - 1.82: 199 Bond restraints: 19205 Sorted by residual: bond pdb=" C4 ADP A1001 " pdb=" C5 ADP A1001 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C4 ADP B1001 " pdb=" C5 ADP B1001 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C5 ADP B1001 " pdb=" C6 ADP B1001 " ideal model delta sigma weight residual 1.490 1.404 0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C5 ADP A1001 " pdb=" C6 ADP A1001 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" O3 PO4 A1002 " pdb=" P PO4 A1002 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.05e+00 ... (remaining 19200 not shown) Histogram of bond angle deviations from ideal: 97.11 - 104.49: 287 104.49 - 111.87: 8849 111.87 - 119.25: 6885 119.25 - 126.63: 9638 126.63 - 134.01: 195 Bond angle restraints: 25854 Sorted by residual: angle pdb=" C GLN A 454 " pdb=" CA GLN A 454 " pdb=" CB GLN A 454 " ideal model delta sigma weight residual 115.89 109.70 6.19 1.32e+00 5.74e-01 2.20e+01 angle pdb=" N VAL B 133 " pdb=" CA VAL B 133 " pdb=" C VAL B 133 " ideal model delta sigma weight residual 113.71 109.76 3.95 9.50e-01 1.11e+00 1.73e+01 angle pdb=" N LEU B 881 " pdb=" CA LEU B 881 " pdb=" C LEU B 881 " ideal model delta sigma weight residual 111.07 107.06 4.01 1.07e+00 8.73e-01 1.40e+01 angle pdb=" C ILE B 356 " pdb=" N MET B 357 " pdb=" CA MET B 357 " ideal model delta sigma weight residual 121.14 115.16 5.98 1.75e+00 3.27e-01 1.17e+01 angle pdb=" C1' ADP A1001 " pdb=" C2' ADP A1001 " pdb=" C3' ADP A1001 " ideal model delta sigma weight residual 111.00 100.82 10.18 3.00e+00 1.11e-01 1.15e+01 ... (remaining 25849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.97: 11218 28.97 - 57.93: 437 57.93 - 86.90: 30 86.90 - 115.86: 2 115.86 - 144.83: 4 Dihedral angle restraints: 11691 sinusoidal: 4928 harmonic: 6763 Sorted by residual: dihedral pdb=" O1B ADP A1001 " pdb=" O3A ADP A1001 " pdb=" PB ADP A1001 " pdb=" PA ADP A1001 " ideal model delta sinusoidal sigma weight residual -60.00 84.83 -144.83 1 2.00e+01 2.50e-03 4.36e+01 dihedral pdb=" O2A ADP A1001 " pdb=" O3A ADP A1001 " pdb=" PA ADP A1001 " pdb=" PB ADP A1001 " ideal model delta sinusoidal sigma weight residual -60.00 75.23 -135.23 1 2.00e+01 2.50e-03 4.10e+01 dihedral pdb=" O2A ADP B1001 " pdb=" O3A ADP B1001 " pdb=" PA ADP B1001 " pdb=" PB ADP B1001 " ideal model delta sinusoidal sigma weight residual -60.00 65.54 -125.54 1 2.00e+01 2.50e-03 3.79e+01 ... (remaining 11688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2255 0.050 - 0.100: 442 0.100 - 0.150: 90 0.150 - 0.199: 5 0.199 - 0.249: 3 Chirality restraints: 2795 Sorted by residual: chirality pdb=" C3' ADP B1001 " pdb=" C2' ADP B1001 " pdb=" C4' ADP B1001 " pdb=" O3' ADP B1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.76 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA LEU B 881 " pdb=" N LEU B 881 " pdb=" C LEU B 881 " pdb=" CB LEU B 881 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" C3' ADP A1001 " pdb=" C2' ADP A1001 " pdb=" C4' ADP A1001 " pdb=" O3' ADP A1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.73 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 2792 not shown) Planarity restraints: 3346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 47 " -0.053 5.00e-02 4.00e+02 7.88e-02 9.94e+00 pdb=" N PRO D 48 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO D 48 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 48 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 111 " 0.012 2.00e-02 2.50e+03 1.72e-02 5.18e+00 pdb=" CG PHE C 111 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE C 111 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 111 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE C 111 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 111 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 111 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 666 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO A 667 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 667 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 667 " -0.030 5.00e-02 4.00e+02 ... (remaining 3343 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 148 2.43 - 3.05: 12576 3.05 - 3.66: 31735 3.66 - 4.28: 44830 4.28 - 4.90: 72213 Nonbonded interactions: 161502 Sorted by model distance: nonbonded pdb=" O2B ADP B1001 " pdb="MG MG B1003 " model vdw 1.812 2.170 nonbonded pdb=" O2B ADP A1001 " pdb="MG MG A1003 " model vdw 1.960 2.170 nonbonded pdb=" OG SER A 242 " pdb="MG MG A1003 " model vdw 2.038 2.170 nonbonded pdb=" O3 PO4 B1002 " pdb="MG MG B1003 " model vdw 2.058 2.170 nonbonded pdb=" OG1 THR B 185 " pdb="MG MG B1003 " model vdw 2.063 2.170 ... (remaining 161497 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 3 through 162 or resid 164 through 198 or resid 216 throug \ h 368 or resid 371 through 406 or resid 410 through 898 or resid 1001 through 10 \ 03)) selection = (chain 'B' and (resid 3 through 162 or resid 164 through 624 or resid 645 throug \ h 898 or resid 1001 through 1003)) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 20 through 143 or resid 149 through 162)) selection = (chain 'F' and (resid 20 through 56 or resid 60 through 143 or resid 149 through \ 162)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 10.730 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: 0.020 Extract box with map and model: 27.450 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 53.460 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 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 : 0.003 0.111 19205 Z= 0.221 Angle : 0.639 10.178 25854 Z= 0.321 Chirality : 0.041 0.249 2795 Planarity : 0.004 0.079 3346 Dihedral : 14.828 144.830 7313 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % 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: 0.58 (0.18), residues: 2283 helix: 1.19 (0.15), residues: 1295 sheet: -0.84 (0.39), residues: 163 loop : -0.54 (0.22), residues: 825 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 432 time to evaluate : 2.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 0.3688 time to fit residues: 229.1453 Evaluate side-chains 253 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 2.242 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 193 optimal weight: 0.1980 chunk 173 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 117 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 69 optimal weight: 0.0370 chunk 109 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 chunk 207 optimal weight: 1.9990 overall best weight: 0.8462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 ASN ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 ASN ** B 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 HIS ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 19205 Z= 0.201 Angle : 0.679 12.624 25854 Z= 0.338 Chirality : 0.042 0.186 2795 Planarity : 0.004 0.049 3346 Dihedral : 7.488 148.955 2534 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.18), residues: 2283 helix: 0.91 (0.14), residues: 1278 sheet: -0.67 (0.40), residues: 161 loop : -0.62 (0.22), residues: 844 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 268 time to evaluate : 2.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 275 average time/residue: 0.3408 time to fit residues: 139.9238 Evaluate side-chains 216 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 210 time to evaluate : 2.147 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1866 time to fit residues: 5.1439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 115 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 173 optimal weight: 7.9990 chunk 141 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 208 optimal weight: 0.9990 chunk 225 optimal weight: 20.0000 chunk 185 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 ASN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 GLN D 50 GLN ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 HIS ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 19205 Z= 0.230 Angle : 0.679 16.905 25854 Z= 0.337 Chirality : 0.042 0.155 2795 Planarity : 0.004 0.049 3346 Dihedral : 7.496 156.258 2534 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.18), residues: 2283 helix: 0.76 (0.14), residues: 1297 sheet: -0.69 (0.40), residues: 159 loop : -0.80 (0.22), residues: 827 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 228 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 238 average time/residue: 0.3102 time to fit residues: 115.1426 Evaluate side-chains 213 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 202 time to evaluate : 2.237 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2063 time to fit residues: 7.1533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 205 optimal weight: 0.0000 chunk 156 optimal weight: 0.2980 chunk 108 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 209 optimal weight: 0.0970 chunk 221 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 198 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 19205 Z= 0.163 Angle : 0.638 14.002 25854 Z= 0.314 Chirality : 0.041 0.223 2795 Planarity : 0.004 0.049 3346 Dihedral : 7.317 152.132 2534 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 0.89 % 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: 0.13 (0.18), residues: 2283 helix: 0.81 (0.14), residues: 1293 sheet: -0.75 (0.40), residues: 160 loop : -0.79 (0.22), residues: 830 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 228 time to evaluate : 2.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 5 residues processed: 241 average time/residue: 0.2975 time to fit residues: 112.3898 Evaluate side-chains 203 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 198 time to evaluate : 2.198 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1832 time to fit residues: 4.7117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 184 optimal weight: 2.9990 chunk 125 optimal weight: 0.1980 chunk 3 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 188 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 198 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 19205 Z= 0.243 Angle : 0.690 15.237 25854 Z= 0.340 Chirality : 0.042 0.189 2795 Planarity : 0.004 0.049 3346 Dihedral : 7.417 157.990 2534 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 21.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.18), residues: 2283 helix: 0.65 (0.14), residues: 1294 sheet: -0.67 (0.41), residues: 154 loop : -0.84 (0.22), residues: 835 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 210 time to evaluate : 2.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 225 average time/residue: 0.3106 time to fit residues: 108.8107 Evaluate side-chains 206 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 196 time to evaluate : 2.253 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2170 time to fit residues: 6.9064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 74 optimal weight: 0.7980 chunk 199 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 221 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 116 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 ASN ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 19205 Z= 0.215 Angle : 0.674 13.426 25854 Z= 0.332 Chirality : 0.042 0.185 2795 Planarity : 0.004 0.059 3346 Dihedral : 7.398 157.714 2534 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.18), residues: 2283 helix: 0.58 (0.14), residues: 1297 sheet: -0.89 (0.40), residues: 156 loop : -0.79 (0.22), residues: 830 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 208 time to evaluate : 2.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 3 residues processed: 219 average time/residue: 0.3128 time to fit residues: 106.7903 Evaluate side-chains 192 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 189 time to evaluate : 2.236 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2101 time to fit residues: 4.2105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 213 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 chunk 161 optimal weight: 5.9990 chunk 125 optimal weight: 0.0060 chunk 186 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 134 optimal weight: 0.9980 chunk 101 optimal weight: 8.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 ASN ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.097 19205 Z= 0.343 Angle : 0.797 15.998 25854 Z= 0.398 Chirality : 0.045 0.250 2795 Planarity : 0.005 0.055 3346 Dihedral : 7.874 167.148 2534 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 26.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.17), residues: 2283 helix: 0.14 (0.14), residues: 1302 sheet: -0.88 (0.42), residues: 138 loop : -1.08 (0.21), residues: 843 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 212 time to evaluate : 2.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 223 average time/residue: 0.3216 time to fit residues: 110.9492 Evaluate side-chains 202 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 192 time to evaluate : 2.379 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2478 time to fit residues: 7.2729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 136 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 ASN ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 19205 Z= 0.199 Angle : 0.705 13.745 25854 Z= 0.348 Chirality : 0.043 0.274 2795 Planarity : 0.004 0.050 3346 Dihedral : 7.580 165.583 2534 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.17), residues: 2283 helix: 0.37 (0.14), residues: 1307 sheet: -1.04 (0.42), residues: 138 loop : -0.96 (0.22), residues: 838 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 197 time to evaluate : 2.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 206 average time/residue: 0.3040 time to fit residues: 99.2249 Evaluate side-chains 192 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 183 time to evaluate : 2.228 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1925 time to fit residues: 7.2269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 200 optimal weight: 0.2980 chunk 211 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 chunk 205 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 89 optimal weight: 0.0970 chunk 161 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 204 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 ASN B 444 ASN ** B 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 19205 Z= 0.186 Angle : 0.709 15.878 25854 Z= 0.348 Chirality : 0.042 0.227 2795 Planarity : 0.004 0.050 3346 Dihedral : 7.384 171.051 2534 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.18), residues: 2283 helix: 0.47 (0.14), residues: 1297 sheet: -0.93 (0.40), residues: 145 loop : -0.79 (0.22), residues: 841 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 199 time to evaluate : 2.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 202 average time/residue: 0.3127 time to fit residues: 99.6092 Evaluate side-chains 190 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 187 time to evaluate : 2.462 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1936 time to fit residues: 4.1555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 135 optimal weight: 8.9990 chunk 217 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 228 optimal weight: 10.0000 chunk 209 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 ASN ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.5105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 19205 Z= 0.272 Angle : 0.743 14.931 25854 Z= 0.369 Chirality : 0.043 0.214 2795 Planarity : 0.004 0.051 3346 Dihedral : 7.523 179.569 2534 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 22.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.18), residues: 2283 helix: 0.38 (0.14), residues: 1300 sheet: -1.00 (0.40), residues: 148 loop : -0.86 (0.22), residues: 835 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4566 Ramachandran restraints generated. 2283 Oldfield, 0 Emsley, 2283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 191 time to evaluate : 2.236 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 192 average time/residue: 0.3056 time to fit residues: 93.2111 Evaluate side-chains 186 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 183 time to evaluate : 2.191 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2224 time to fit residues: 4.1660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 144 optimal weight: 8.9990 chunk 193 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 167 optimal weight: 0.4980 chunk 26 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 181 optimal weight: 0.0870 chunk 76 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 ASN ** B 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.076155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.060695 restraints weight = 167761.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.062550 restraints weight = 78580.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.063764 restraints weight = 47486.037| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3757 r_free = 0.3757 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3757 r_free = 0.3757 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 19205 Z= 0.185 Angle : 0.731 15.056 25854 Z= 0.361 Chirality : 0.043 0.229 2795 Planarity : 0.004 0.050 3346 Dihedral : 7.174 167.957 2534 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.18), residues: 2283 helix: 0.41 (0.14), residues: 1292 sheet: -1.01 (0.42), residues: 135 loop : -0.78 (0.22), residues: 856 =============================================================================== Job complete usr+sys time: 4044.04 seconds wall clock time: 74 minutes 48.66 seconds (4488.66 seconds total)