Starting phenix.real_space_refine on Sun Mar 17 20:30:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8act_15353/03_2024/8act_15353_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8act_15353/03_2024/8act_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_15353/03_2024/8act_15353.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8act_15353/03_2024/8act_15353.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8act_15353/03_2024/8act_15353_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8act_15353/03_2024/8act_15353_updated.pdb" } resolution = 3.6 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= 0.024 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 12.54, per 1000 atoms: 0.67 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: 7.96 Conformation dependent library (CDL) restraints added in 4.4 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: 4.89 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: 6.17 Time building geometry restraints manager: 8.49 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: 10.240 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: 0.000 Extract box with map and model: 30.060 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 54.160 Find NCS groups from input model: 1.110 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: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.550 ------------------------------------------------------------------------------- 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 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 816 HIS 0.003 0.001 HIS B 556 PHE 0.039 0.001 PHE C 111 TYR 0.017 0.001 TYR E 118 ARG 0.003 0.000 ARG E 120 *********************** 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 : 2.206 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 REVERT: A 350 TYR cc_start: 0.7931 (m-80) cc_final: 0.7317 (m-80) REVERT: A 413 LYS cc_start: 0.7321 (tptp) cc_final: 0.7010 (tmtt) REVERT: A 690 MET cc_start: 0.7877 (tmm) cc_final: 0.7570 (tmm) REVERT: A 700 GLU cc_start: 0.8677 (mp0) cc_final: 0.8360 (mp0) REVERT: A 811 LEU cc_start: 0.8568 (mt) cc_final: 0.8353 (pp) REVERT: A 849 MET cc_start: 0.7981 (ptp) cc_final: 0.7052 (tpt) REVERT: A 852 MET cc_start: 0.8949 (tpp) cc_final: 0.8540 (tpp) REVERT: A 877 MET cc_start: 0.7447 (mmt) cc_final: 0.6018 (mmt) REVERT: A 889 LEU cc_start: 0.9341 (mt) cc_final: 0.9031 (tt) REVERT: B 6 MET cc_start: 0.5534 (mmt) cc_final: 0.5216 (mmt) REVERT: B 113 MET cc_start: 0.7565 (mtp) cc_final: 0.7180 (mtm) REVERT: B 312 PHE cc_start: 0.6053 (m-10) cc_final: 0.5663 (m-80) REVERT: B 435 MET cc_start: 0.8152 (tmm) cc_final: 0.7713 (tmm) REVERT: B 439 MET cc_start: 0.8375 (mtp) cc_final: 0.7915 (mtp) REVERT: B 531 MET cc_start: 0.7498 (ttt) cc_final: 0.6975 (tpp) REVERT: B 536 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8786 (tm-30) REVERT: B 606 VAL cc_start: 0.8508 (t) cc_final: 0.8178 (t) REVERT: B 799 MET cc_start: 0.7779 (mpp) cc_final: 0.7024 (ppp) REVERT: B 804 LEU cc_start: 0.8984 (tp) cc_final: 0.8674 (mt) REVERT: B 811 LEU cc_start: 0.9192 (mt) cc_final: 0.8974 (tp) REVERT: B 834 PHE cc_start: 0.6558 (t80) cc_final: 0.5843 (t80) REVERT: B 852 MET cc_start: 0.8454 (ppp) cc_final: 0.8139 (ppp) REVERT: C 59 MET cc_start: 0.7710 (mmm) cc_final: 0.6872 (mmm) REVERT: C 69 MET cc_start: 0.6723 (mpp) cc_final: 0.5591 (tpt) REVERT: C 117 MET cc_start: 0.7066 (tpt) cc_final: 0.6851 (tpt) REVERT: D 56 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6455 (tp30) REVERT: D 109 MET cc_start: 0.9027 (mmm) cc_final: 0.8745 (mmt) REVERT: D 140 PHE cc_start: 0.7676 (m-80) cc_final: 0.6989 (m-80) REVERT: D 142 LYS cc_start: 0.3240 (mmtt) cc_final: 0.2702 (mmmt) REVERT: E 36 MET cc_start: 0.8812 (mmp) cc_final: 0.8595 (mmp) REVERT: E 130 PHE cc_start: 0.6949 (m-80) cc_final: 0.6426 (m-80) REVERT: E 139 PHE cc_start: 0.7024 (m-80) cc_final: 0.6538 (m-80) REVERT: F 20 MET cc_start: 0.4415 (ppp) cc_final: 0.1062 (mmm) REVERT: F 26 ILE cc_start: 0.7394 (pt) cc_final: 0.6988 (pt) REVERT: F 34 THR cc_start: 0.8184 (m) cc_final: 0.7440 (m) REVERT: F 40 ARG cc_start: 0.7167 (mmp-170) cc_final: 0.6399 (ptt-90) REVERT: F 69 MET cc_start: 0.0142 (mmt) cc_final: -0.0317 (mmp) REVERT: F 113 VAL cc_start: 0.6650 (m) cc_final: 0.6199 (p) REVERT: F 156 VAL cc_start: 0.9226 (t) cc_final: 0.9019 (m) outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 0.3653 time to fit residues: 226.3602 Evaluate side-chains 260 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 2.096 ------------------------------------------------------------------------------- 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: 1.9990 chunk 173 optimal weight: 6.9990 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: 6.9990 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: 1.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 78 ASN E 157 HIS ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19205 Z= 0.214 Angle : 0.662 13.071 25854 Z= 0.331 Chirality : 0.042 0.192 2795 Planarity : 0.004 0.049 3346 Dihedral : 7.465 151.974 2534 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.79 % Allowed : 10.22 % Favored : 88.99 % 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: 0.29 (0.18), residues: 2283 helix: 0.95 (0.14), residues: 1288 sheet: -0.68 (0.40), residues: 161 loop : -0.72 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 816 HIS 0.010 0.001 HIS B 581 PHE 0.037 0.002 PHE C 61 TYR 0.023 0.002 TYR E 118 ARG 0.008 0.001 ARG A 694 *********************** 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 286 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 270 time to evaluate : 2.221 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: A 77 MET cc_start: 0.7635 (mmt) cc_final: 0.7258 (mmt) REVERT: A 350 TYR cc_start: 0.8038 (m-80) cc_final: 0.7450 (m-80) REVERT: A 413 LYS cc_start: 0.7339 (tptp) cc_final: 0.6979 (tmtt) REVERT: A 699 LEU cc_start: 0.8899 (tp) cc_final: 0.8586 (tp) REVERT: A 700 GLU cc_start: 0.8698 (mp0) cc_final: 0.8148 (mp0) REVERT: A 776 MET cc_start: 0.9417 (mtm) cc_final: 0.9200 (mtm) REVERT: A 849 MET cc_start: 0.8017 (ptp) cc_final: 0.7082 (tpt) REVERT: A 892 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8226 (mt0) REVERT: B 6 MET cc_start: 0.5523 (mmt) cc_final: 0.5258 (mmt) REVERT: B 113 MET cc_start: 0.7574 (mtp) cc_final: 0.7225 (mtm) REVERT: B 435 MET cc_start: 0.8163 (tmm) cc_final: 0.7918 (tmm) REVERT: B 439 MET cc_start: 0.8366 (mtp) cc_final: 0.8112 (mtp) REVERT: B 536 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8733 (tm-30) REVERT: B 811 LEU cc_start: 0.9132 (mt) cc_final: 0.8591 (tp) REVERT: B 821 PHE cc_start: 0.8286 (t80) cc_final: 0.7719 (t80) REVERT: B 852 MET cc_start: 0.8698 (ppp) cc_final: 0.8346 (ppp) REVERT: C 59 MET cc_start: 0.7863 (mmm) cc_final: 0.7360 (mmm) REVERT: C 69 MET cc_start: 0.6754 (mpp) cc_final: 0.5514 (tpt) REVERT: D 51 ILE cc_start: 0.5466 (mm) cc_final: 0.5137 (mm) REVERT: D 56 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6494 (tp30) REVERT: D 62 ASP cc_start: 0.5358 (OUTLIER) cc_final: 0.4498 (p0) REVERT: D 140 PHE cc_start: 0.7599 (m-80) cc_final: 0.6962 (m-80) REVERT: D 142 LYS cc_start: 0.3877 (mmtt) cc_final: 0.3087 (mmmt) REVERT: E 85 MET cc_start: 0.5518 (tmm) cc_final: 0.5209 (tmm) REVERT: E 118 TYR cc_start: 0.7940 (t80) cc_final: 0.7557 (t80) REVERT: E 122 MET cc_start: 0.8005 (mtm) cc_final: 0.6285 (tpt) REVERT: E 139 PHE cc_start: 0.6706 (m-80) cc_final: 0.6346 (m-80) REVERT: F 20 MET cc_start: 0.4386 (ppp) cc_final: 0.0851 (mmm) REVERT: F 26 ILE cc_start: 0.7444 (pt) cc_final: 0.7022 (pt) REVERT: F 34 THR cc_start: 0.8167 (m) cc_final: 0.7411 (m) REVERT: F 40 ARG cc_start: 0.7177 (mmp-170) cc_final: 0.6392 (ptt-90) REVERT: F 69 MET cc_start: 0.0118 (mmt) cc_final: -0.0425 (mmp) REVERT: F 138 MET cc_start: 0.6911 (tpt) cc_final: 0.6677 (mmm) outliers start: 16 outliers final: 10 residues processed: 278 average time/residue: 0.3351 time to fit residues: 139.4072 Evaluate side-chains 231 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 220 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 833 TYR Chi-restraints excluded: chain B residue 874 GLU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 100 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 115 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 141 optimal weight: 8.9990 chunk 57 optimal weight: 0.7980 chunk 208 optimal weight: 10.0000 chunk 225 optimal weight: 4.9990 chunk 185 optimal weight: 0.0000 chunk 206 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 167 optimal weight: 9.9990 overall best weight: 1.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 GLN A 479 ASN ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 ASN ** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 ASN ** B 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN ** 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** C 101 GLN ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7082 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 19205 Z= 0.235 Angle : 0.656 10.328 25854 Z= 0.330 Chirality : 0.042 0.174 2795 Planarity : 0.004 0.064 3346 Dihedral : 7.498 156.875 2534 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.33 % Allowed : 13.13 % Favored : 85.54 % 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: 0.02 (0.18), residues: 2283 helix: 0.70 (0.14), residues: 1303 sheet: -0.80 (0.40), residues: 161 loop : -0.81 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 130 HIS 0.009 0.001 HIS B 581 PHE 0.026 0.002 PHE C 61 TYR 0.025 0.002 TYR A 609 ARG 0.008 0.001 ARG A 807 *********************** 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 260 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 233 time to evaluate : 2.335 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: A 77 MET cc_start: 0.7697 (mmt) cc_final: 0.7133 (mmt) REVERT: A 113 MET cc_start: 0.6891 (mmt) cc_final: 0.6132 (mmt) REVERT: A 350 TYR cc_start: 0.8087 (m-80) cc_final: 0.7460 (m-80) REVERT: A 413 LYS cc_start: 0.7329 (tptp) cc_final: 0.6903 (tmtt) REVERT: A 700 GLU cc_start: 0.8778 (mp0) cc_final: 0.8036 (mp0) REVERT: A 849 MET cc_start: 0.8031 (ptp) cc_final: 0.7146 (tpt) REVERT: B 113 MET cc_start: 0.7628 (mtp) cc_final: 0.7228 (mtm) REVERT: B 330 MET cc_start: 0.8296 (ppp) cc_final: 0.8036 (ppp) REVERT: B 435 MET cc_start: 0.8443 (tmm) cc_final: 0.7936 (tmm) REVERT: B 436 PHE cc_start: 0.8773 (t80) cc_final: 0.8275 (t80) REVERT: B 536 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8712 (tm-30) REVERT: B 811 LEU cc_start: 0.9132 (mt) cc_final: 0.8573 (tp) REVERT: B 821 PHE cc_start: 0.8316 (t80) cc_final: 0.7814 (t80) REVERT: B 852 MET cc_start: 0.8712 (ppp) cc_final: 0.8408 (ppp) REVERT: C 59 MET cc_start: 0.7916 (mmm) cc_final: 0.7155 (mmm) REVERT: C 69 MET cc_start: 0.6778 (mpp) cc_final: 0.5502 (tpt) REVERT: C 94 ARG cc_start: 0.8253 (ptt-90) cc_final: 0.7980 (ptt-90) REVERT: D 56 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6391 (tp30) REVERT: D 69 MET cc_start: 0.5388 (mmm) cc_final: 0.5168 (tpp) REVERT: D 140 PHE cc_start: 0.7598 (m-80) cc_final: 0.6960 (m-80) REVERT: D 142 LYS cc_start: 0.3784 (mmtt) cc_final: 0.3011 (mmmt) REVERT: E 85 MET cc_start: 0.5484 (tmm) cc_final: 0.5092 (tmm) REVERT: E 118 TYR cc_start: 0.7916 (t80) cc_final: 0.7594 (t80) REVERT: E 122 MET cc_start: 0.8014 (mtm) cc_final: 0.6383 (tpt) REVERT: E 130 PHE cc_start: 0.7100 (m-80) cc_final: 0.6515 (m-80) REVERT: E 139 PHE cc_start: 0.6671 (m-80) cc_final: 0.6292 (m-80) REVERT: F 20 MET cc_start: 0.4573 (ppp) cc_final: 0.0664 (mmm) REVERT: F 26 ILE cc_start: 0.7231 (pt) cc_final: 0.7002 (pt) REVERT: F 34 THR cc_start: 0.8134 (m) cc_final: 0.7336 (m) REVERT: F 40 ARG cc_start: 0.7077 (mmp-170) cc_final: 0.6328 (ptt-90) REVERT: F 69 MET cc_start: 0.0267 (mmt) cc_final: 0.0055 (tpp) outliers start: 27 outliers final: 14 residues processed: 248 average time/residue: 0.3194 time to fit residues: 122.2013 Evaluate side-chains 217 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 203 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 833 TYR Chi-restraints excluded: chain B residue 874 GLU Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 100 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 205 optimal weight: 0.8980 chunk 156 optimal weight: 0.0980 chunk 108 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 209 optimal weight: 5.9990 chunk 221 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 198 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- 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 232 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 487 GLN ** 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** ** E 161 HIS ** 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: 0.7163 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 19205 Z= 0.290 Angle : 0.700 12.842 25854 Z= 0.351 Chirality : 0.043 0.181 2795 Planarity : 0.005 0.049 3346 Dihedral : 7.655 161.345 2534 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 23.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.12 % Allowed : 15.45 % Favored : 82.43 % 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: -0.23 (0.17), residues: 2283 helix: 0.49 (0.14), residues: 1298 sheet: -0.97 (0.39), residues: 158 loop : -0.88 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 829 HIS 0.006 0.001 HIS B 581 PHE 0.027 0.002 PHE C 61 TYR 0.018 0.002 TYR A 609 ARG 0.011 0.001 ARG B 652 *********************** 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 264 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 221 time to evaluate : 2.209 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: A 77 MET cc_start: 0.7929 (mmt) cc_final: 0.7543 (mmt) REVERT: A 350 TYR cc_start: 0.8223 (m-80) cc_final: 0.7564 (m-80) REVERT: A 413 LYS cc_start: 0.7164 (tptp) cc_final: 0.6636 (tmtt) REVERT: B 43 LYS cc_start: 0.8108 (mmtp) cc_final: 0.7588 (mmmt) REVERT: B 113 MET cc_start: 0.7557 (mtp) cc_final: 0.7187 (mtm) REVERT: B 179 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6695 (tp30) REVERT: B 312 PHE cc_start: 0.6181 (m-10) cc_final: 0.5807 (m-80) REVERT: B 330 MET cc_start: 0.8272 (ppp) cc_final: 0.8014 (ptp) REVERT: B 418 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8108 (pp30) REVERT: B 422 TYR cc_start: 0.7454 (m-80) cc_final: 0.6891 (m-80) REVERT: B 435 MET cc_start: 0.8542 (tmm) cc_final: 0.8264 (tmm) REVERT: B 536 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8638 (tm-30) REVERT: B 811 LEU cc_start: 0.9075 (mt) cc_final: 0.8491 (tp) REVERT: B 821 PHE cc_start: 0.8447 (t80) cc_final: 0.7862 (t80) REVERT: B 852 MET cc_start: 0.8775 (ppp) cc_final: 0.8067 (ppp) REVERT: C 59 MET cc_start: 0.7906 (mmm) cc_final: 0.7409 (mmm) REVERT: C 61 PHE cc_start: 0.7012 (t80) cc_final: 0.6741 (t80) REVERT: C 69 MET cc_start: 0.6647 (mpp) cc_final: 0.5275 (tpt) REVERT: D 56 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6499 (tp30) REVERT: D 140 PHE cc_start: 0.7672 (m-80) cc_final: 0.6982 (m-80) REVERT: D 142 LYS cc_start: 0.3814 (mmtt) cc_final: 0.2960 (mmmt) REVERT: E 65 GLU cc_start: 0.6330 (tt0) cc_final: 0.6041 (mp0) REVERT: E 118 TYR cc_start: 0.7850 (t80) cc_final: 0.7543 (t80) REVERT: E 122 MET cc_start: 0.7922 (mtm) cc_final: 0.6495 (tpp) REVERT: F 20 MET cc_start: 0.4657 (ppp) cc_final: 0.0684 (tpt) REVERT: F 26 ILE cc_start: 0.7274 (pt) cc_final: 0.7054 (pt) REVERT: F 34 THR cc_start: 0.8132 (m) cc_final: 0.7486 (p) REVERT: F 40 ARG cc_start: 0.7002 (mmp-170) cc_final: 0.6105 (ptt-90) REVERT: F 69 MET cc_start: 0.0344 (mmt) cc_final: -0.0167 (mmp) outliers start: 43 outliers final: 21 residues processed: 247 average time/residue: 0.2998 time to fit residues: 113.8934 Evaluate side-chains 226 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 204 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 610 GLN Chi-restraints excluded: chain B residue 833 TYR Chi-restraints excluded: chain B residue 874 GLU Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 86 ASN Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 27 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 184 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 164 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 188 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 198 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 ASN ** 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 50 GLN ** D 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19205 Z= 0.177 Angle : 0.642 12.585 25854 Z= 0.318 Chirality : 0.041 0.166 2795 Planarity : 0.004 0.049 3346 Dihedral : 7.450 158.192 2534 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.78 % Allowed : 16.83 % Favored : 81.39 % 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: -0.02 (0.18), residues: 2283 helix: 0.67 (0.15), residues: 1283 sheet: -1.01 (0.41), residues: 147 loop : -0.74 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 130 HIS 0.008 0.001 HIS B 581 PHE 0.022 0.001 PHE C 61 TYR 0.018 0.001 TYR A 609 ARG 0.011 0.000 ARG A 858 *********************** 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 259 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 223 time to evaluate : 2.199 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: A 77 MET cc_start: 0.7840 (mmt) cc_final: 0.7443 (mmt) REVERT: A 113 MET cc_start: 0.6977 (mmt) cc_final: 0.6706 (mmt) REVERT: A 350 TYR cc_start: 0.8143 (m-80) cc_final: 0.7523 (m-80) REVERT: A 413 LYS cc_start: 0.7151 (tptp) cc_final: 0.6635 (tmtt) REVERT: A 861 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8297 (mm-30) REVERT: B 43 LYS cc_start: 0.8073 (mmtp) cc_final: 0.7565 (mmmt) REVERT: B 113 MET cc_start: 0.7600 (mtp) cc_final: 0.7220 (mtm) REVERT: B 165 MET cc_start: 0.8587 (tpp) cc_final: 0.8234 (tpt) REVERT: B 312 PHE cc_start: 0.6203 (m-10) cc_final: 0.5865 (m-80) REVERT: B 418 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.7839 (pt0) REVERT: B 422 TYR cc_start: 0.7466 (m-80) cc_final: 0.6884 (m-80) REVERT: B 435 MET cc_start: 0.8406 (tmm) cc_final: 0.7812 (tmm) REVERT: B 447 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7231 (mm) REVERT: B 536 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8656 (tm-30) REVERT: B 811 LEU cc_start: 0.9028 (mt) cc_final: 0.8450 (tp) REVERT: B 821 PHE cc_start: 0.8402 (t80) cc_final: 0.8006 (t80) REVERT: B 852 MET cc_start: 0.8808 (ppp) cc_final: 0.8548 (ppp) REVERT: C 59 MET cc_start: 0.7914 (mmm) cc_final: 0.7431 (mmm) REVERT: C 69 MET cc_start: 0.6855 (mpp) cc_final: 0.5477 (tpt) REVERT: D 56 GLU cc_start: 0.7305 (mm-30) cc_final: 0.6488 (tp30) REVERT: D 69 MET cc_start: 0.5054 (mmm) cc_final: 0.3933 (mmm) REVERT: D 140 PHE cc_start: 0.7643 (m-80) cc_final: 0.6929 (m-80) REVERT: D 142 LYS cc_start: 0.3820 (mmtt) cc_final: 0.3061 (mmmt) REVERT: E 65 GLU cc_start: 0.6339 (tt0) cc_final: 0.5985 (mp0) REVERT: E 85 MET cc_start: 0.5356 (tmm) cc_final: 0.5063 (tmm) REVERT: E 118 TYR cc_start: 0.7799 (t80) cc_final: 0.7481 (t80) REVERT: E 122 MET cc_start: 0.7948 (mtm) cc_final: 0.6508 (tpt) REVERT: F 20 MET cc_start: 0.4711 (ppp) cc_final: 0.0614 (mmm) REVERT: F 26 ILE cc_start: 0.7410 (pt) cc_final: 0.7196 (pt) REVERT: F 34 THR cc_start: 0.8121 (m) cc_final: 0.7387 (m) REVERT: F 40 ARG cc_start: 0.7074 (mmp-170) cc_final: 0.6522 (ptt-90) REVERT: F 69 MET cc_start: 0.0468 (mmt) cc_final: -0.0143 (mmp) outliers start: 36 outliers final: 22 residues processed: 244 average time/residue: 0.3009 time to fit residues: 113.4236 Evaluate side-chains 229 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 205 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 833 TYR Chi-restraints excluded: chain B residue 874 GLU Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 36 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 74 optimal weight: 0.8980 chunk 199 optimal weight: 0.2980 chunk 43 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 221 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 116 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 ASN ** 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: 0.7128 moved from start: 0.3908 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= 0.174 Angle : 0.627 12.310 25854 Z= 0.310 Chirality : 0.040 0.169 2795 Planarity : 0.004 0.049 3346 Dihedral : 7.315 160.321 2534 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.63 % Allowed : 17.82 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.18), residues: 2283 helix: 0.72 (0.15), residues: 1285 sheet: -0.83 (0.40), residues: 154 loop : -0.73 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 816 HIS 0.006 0.001 HIS B 581 PHE 0.028 0.001 PHE C 61 TYR 0.017 0.001 TYR A 609 ARG 0.008 0.000 ARG A 858 *********************** 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 247 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 214 time to evaluate : 2.220 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: A 77 MET cc_start: 0.7856 (mmt) cc_final: 0.7393 (mmt) REVERT: A 350 TYR cc_start: 0.8147 (m-80) cc_final: 0.7540 (m-80) REVERT: A 413 LYS cc_start: 0.7122 (tptp) cc_final: 0.6582 (tmtt) REVERT: A 776 MET cc_start: 0.9478 (mtt) cc_final: 0.9189 (mpp) REVERT: A 865 LYS cc_start: 0.9371 (tppt) cc_final: 0.9056 (pttp) REVERT: B 43 LYS cc_start: 0.8078 (mmtp) cc_final: 0.7579 (mmmt) REVERT: B 113 MET cc_start: 0.7588 (mtp) cc_final: 0.7216 (mtm) REVERT: B 312 PHE cc_start: 0.6280 (m-10) cc_final: 0.5933 (m-80) REVERT: B 418 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8269 (pt0) REVERT: B 435 MET cc_start: 0.8452 (tmm) cc_final: 0.7846 (tmm) REVERT: B 447 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7227 (mm) REVERT: B 536 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8633 (tm-30) REVERT: B 659 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8371 (mtm) REVERT: B 821 PHE cc_start: 0.8401 (t80) cc_final: 0.8020 (t80) REVERT: B 852 MET cc_start: 0.8740 (ppp) cc_final: 0.8529 (ppp) REVERT: C 59 MET cc_start: 0.8064 (mmm) cc_final: 0.7433 (mmm) REVERT: C 69 MET cc_start: 0.6871 (mpp) cc_final: 0.5452 (tpt) REVERT: D 56 GLU cc_start: 0.7317 (mm-30) cc_final: 0.6560 (tp30) REVERT: D 69 MET cc_start: 0.5063 (mmm) cc_final: 0.3952 (mmm) REVERT: D 140 PHE cc_start: 0.7651 (m-80) cc_final: 0.6926 (m-80) REVERT: D 142 LYS cc_start: 0.3849 (mmtt) cc_final: 0.3080 (mmmt) REVERT: E 65 GLU cc_start: 0.6326 (tt0) cc_final: 0.5979 (mp0) REVERT: E 85 MET cc_start: 0.5357 (tmm) cc_final: 0.5057 (tmm) REVERT: E 122 MET cc_start: 0.8003 (mtm) cc_final: 0.7726 (ptp) REVERT: F 20 MET cc_start: 0.4659 (ppp) cc_final: 0.0550 (mmm) REVERT: F 34 THR cc_start: 0.8191 (m) cc_final: 0.7492 (m) REVERT: F 40 ARG cc_start: 0.7017 (mmp-170) cc_final: 0.6562 (ptt-90) REVERT: F 69 MET cc_start: 0.0437 (mmt) cc_final: 0.0126 (mmm) outliers start: 33 outliers final: 23 residues processed: 232 average time/residue: 0.3024 time to fit residues: 110.7965 Evaluate side-chains 229 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 203 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain B residue 292 ASN Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 833 TYR Chi-restraints excluded: chain B residue 874 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain F residue 36 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 213 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 chunk 161 optimal weight: 0.9980 chunk 125 optimal weight: 0.0000 chunk 186 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 220 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 720 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19205 Z= 0.190 Angle : 0.636 14.191 25854 Z= 0.314 Chirality : 0.040 0.162 2795 Planarity : 0.004 0.049 3346 Dihedral : 7.287 163.609 2534 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.68 % Allowed : 18.21 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.18), residues: 2283 helix: 0.67 (0.15), residues: 1294 sheet: -0.86 (0.41), residues: 153 loop : -0.81 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 816 HIS 0.005 0.001 HIS B 581 PHE 0.035 0.001 PHE B 621 TYR 0.016 0.001 TYR A 609 ARG 0.006 0.000 ARG A 858 *********************** 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 242 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 208 time to evaluate : 2.573 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: A 77 MET cc_start: 0.7831 (mmt) cc_final: 0.7518 (mmp) REVERT: A 113 MET cc_start: 0.6942 (mmt) cc_final: 0.6644 (mmt) REVERT: A 350 TYR cc_start: 0.8169 (m-80) cc_final: 0.7570 (m-80) REVERT: A 413 LYS cc_start: 0.7037 (tptp) cc_final: 0.6473 (tmtt) REVERT: A 865 LYS cc_start: 0.9374 (tppt) cc_final: 0.9070 (pttp) REVERT: B 43 LYS cc_start: 0.8026 (mmtp) cc_final: 0.7552 (mmmt) REVERT: B 113 MET cc_start: 0.7524 (mtp) cc_final: 0.7172 (mtm) REVERT: B 165 MET cc_start: 0.8371 (tpp) cc_final: 0.8163 (tpt) REVERT: B 312 PHE cc_start: 0.6255 (m-10) cc_final: 0.5898 (m-80) REVERT: B 330 MET cc_start: 0.8260 (ppp) cc_final: 0.7946 (ptt) REVERT: B 418 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8287 (pt0) REVERT: B 435 MET cc_start: 0.8494 (tmm) cc_final: 0.7894 (tmm) REVERT: B 447 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7245 (mm) REVERT: B 536 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8620 (tm-30) REVERT: B 659 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8393 (mtm) REVERT: B 809 ASP cc_start: 0.9414 (m-30) cc_final: 0.9198 (p0) REVERT: B 821 PHE cc_start: 0.8443 (t80) cc_final: 0.8083 (t80) REVERT: B 846 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8804 (mt-10) REVERT: B 852 MET cc_start: 0.8783 (ppp) cc_final: 0.8436 (ppp) REVERT: C 59 MET cc_start: 0.8055 (mmm) cc_final: 0.7432 (mmm) REVERT: C 69 MET cc_start: 0.6734 (mpp) cc_final: 0.5355 (tpt) REVERT: D 56 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6530 (tp30) REVERT: D 69 MET cc_start: 0.4706 (mmm) cc_final: 0.3610 (mmm) REVERT: D 140 PHE cc_start: 0.7712 (m-80) cc_final: 0.6956 (m-80) REVERT: D 142 LYS cc_start: 0.3811 (mmtt) cc_final: 0.3043 (mmmt) REVERT: E 26 ILE cc_start: 0.8050 (mt) cc_final: 0.7596 (tt) REVERT: E 65 GLU cc_start: 0.6362 (tt0) cc_final: 0.5968 (mp0) REVERT: E 122 MET cc_start: 0.7945 (mtm) cc_final: 0.7692 (ptp) REVERT: F 20 MET cc_start: 0.4635 (ppp) cc_final: 0.0526 (mmm) REVERT: F 34 THR cc_start: 0.8247 (m) cc_final: 0.7564 (m) REVERT: F 40 ARG cc_start: 0.6964 (mmp-170) cc_final: 0.6549 (ptt-90) REVERT: F 69 MET cc_start: 0.0440 (mmt) cc_final: 0.0096 (mmm) outliers start: 34 outliers final: 25 residues processed: 228 average time/residue: 0.2962 time to fit residues: 104.9732 Evaluate side-chains 231 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 203 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 874 GLU Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain F residue 53 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 136 optimal weight: 0.0970 chunk 88 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 0.0770 chunk 42 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 692 GLN ** 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 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 ASN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19205 Z= 0.157 Angle : 0.624 14.490 25854 Z= 0.306 Chirality : 0.040 0.167 2795 Planarity : 0.004 0.049 3346 Dihedral : 7.111 165.905 2534 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.43 % Allowed : 18.66 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.18), residues: 2283 helix: 0.73 (0.15), residues: 1294 sheet: -0.82 (0.40), residues: 153 loop : -0.79 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 816 HIS 0.005 0.001 HIS F 157 PHE 0.024 0.001 PHE C 61 TYR 0.016 0.001 TYR A 609 ARG 0.006 0.000 ARG A 858 *********************** 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 250 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 221 time to evaluate : 2.274 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: A 77 MET cc_start: 0.7797 (mmt) cc_final: 0.7473 (mmp) REVERT: A 113 MET cc_start: 0.6851 (mmt) cc_final: 0.6544 (mmt) REVERT: A 350 TYR cc_start: 0.8108 (m-80) cc_final: 0.7570 (m-80) REVERT: A 405 LYS cc_start: 0.9021 (ttmt) cc_final: 0.8774 (tttp) REVERT: A 865 LYS cc_start: 0.9346 (tppt) cc_final: 0.9045 (pttp) REVERT: B 43 LYS cc_start: 0.8004 (mmtp) cc_final: 0.7598 (mmmt) REVERT: B 113 MET cc_start: 0.7611 (mtp) cc_final: 0.7239 (mtm) REVERT: B 312 PHE cc_start: 0.6336 (m-10) cc_final: 0.5987 (m-10) REVERT: B 330 MET cc_start: 0.8217 (ppp) cc_final: 0.7975 (ptt) REVERT: B 418 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8333 (pt0) REVERT: B 435 MET cc_start: 0.8469 (tmm) cc_final: 0.7972 (tmm) REVERT: B 439 MET cc_start: 0.8258 (mtp) cc_final: 0.7994 (mtp) REVERT: B 447 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.6993 (mm) REVERT: B 536 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8608 (tm-30) REVERT: B 659 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8371 (mtm) REVERT: B 809 ASP cc_start: 0.9379 (m-30) cc_final: 0.9165 (p0) REVERT: B 821 PHE cc_start: 0.8407 (t80) cc_final: 0.8087 (t80) REVERT: B 846 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8796 (mt-10) REVERT: B 852 MET cc_start: 0.8790 (ppp) cc_final: 0.8488 (ppp) REVERT: C 59 MET cc_start: 0.8058 (mmm) cc_final: 0.7438 (mmm) REVERT: C 69 MET cc_start: 0.6937 (mpp) cc_final: 0.5506 (tpt) REVERT: C 102 GLU cc_start: 0.7442 (pm20) cc_final: 0.7228 (pm20) REVERT: D 56 GLU cc_start: 0.7388 (mm-30) cc_final: 0.6706 (tp30) REVERT: D 69 MET cc_start: 0.4519 (mmm) cc_final: 0.3981 (tpp) REVERT: D 140 PHE cc_start: 0.7702 (m-80) cc_final: 0.6941 (m-80) REVERT: D 142 LYS cc_start: 0.4024 (mmtt) cc_final: 0.3266 (mmmt) REVERT: E 65 GLU cc_start: 0.6418 (tt0) cc_final: 0.6068 (mp0) REVERT: E 85 MET cc_start: 0.5403 (tmm) cc_final: 0.5196 (tmm) REVERT: E 118 TYR cc_start: 0.7624 (t80) cc_final: 0.7253 (t80) REVERT: E 122 MET cc_start: 0.8021 (mtm) cc_final: 0.6909 (tpt) REVERT: F 20 MET cc_start: 0.4592 (ppp) cc_final: 0.0525 (mmm) REVERT: F 34 THR cc_start: 0.8201 (m) cc_final: 0.7528 (m) REVERT: F 40 ARG cc_start: 0.7055 (mmp-170) cc_final: 0.6658 (ptt-90) REVERT: F 69 MET cc_start: 0.0391 (mmt) cc_final: 0.0163 (mmm) REVERT: F 90 LEU cc_start: 0.8498 (tp) cc_final: 0.8160 (pp) outliers start: 29 outliers final: 22 residues processed: 239 average time/residue: 0.3087 time to fit residues: 113.8433 Evaluate side-chains 230 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 205 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 833 TYR Chi-restraints excluded: chain B residue 874 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain E residue 84 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 200 optimal weight: 6.9990 chunk 211 optimal weight: 0.0670 chunk 192 optimal weight: 0.8980 chunk 205 optimal weight: 0.9990 chunk 123 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 161 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 overall best weight: 1.1924 ------------------------------------------------------------------------------- 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 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 ASN ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19205 Z= 0.191 Angle : 0.644 14.563 25854 Z= 0.317 Chirality : 0.041 0.252 2795 Planarity : 0.004 0.049 3346 Dihedral : 7.103 172.987 2534 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.63 % Allowed : 18.85 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.18), residues: 2283 helix: 0.70 (0.15), residues: 1301 sheet: -0.88 (0.40), residues: 153 loop : -0.80 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 816 HIS 0.006 0.001 HIS B 401 PHE 0.024 0.001 PHE C 61 TYR 0.016 0.001 TYR A 609 ARG 0.005 0.000 ARG A 858 *********************** 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 245 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 212 time to evaluate : 2.152 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: A 77 MET cc_start: 0.7794 (mmt) cc_final: 0.7293 (mmt) REVERT: A 113 MET cc_start: 0.6834 (mmt) cc_final: 0.6517 (mmt) REVERT: A 350 TYR cc_start: 0.8155 (m-80) cc_final: 0.7572 (m-80) REVERT: A 405 LYS cc_start: 0.9027 (ttmt) cc_final: 0.8782 (tttp) REVERT: A 410 TYR cc_start: 0.7513 (m-80) cc_final: 0.7196 (m-80) REVERT: A 865 LYS cc_start: 0.9358 (tppt) cc_final: 0.9055 (pttp) REVERT: B 43 LYS cc_start: 0.7944 (mmtp) cc_final: 0.7566 (mmmt) REVERT: B 113 MET cc_start: 0.7515 (mtp) cc_final: 0.7186 (mtm) REVERT: B 312 PHE cc_start: 0.6373 (m-10) cc_final: 0.5985 (m-10) REVERT: B 330 MET cc_start: 0.8214 (ppp) cc_final: 0.7980 (ptt) REVERT: B 435 MET cc_start: 0.8479 (tmm) cc_final: 0.7986 (tmm) REVERT: B 439 MET cc_start: 0.8248 (mtp) cc_final: 0.7985 (mtp) REVERT: B 447 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.6972 (mm) REVERT: B 536 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8586 (tm-30) REVERT: B 659 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8379 (mtm) REVERT: B 690 MET cc_start: 0.5715 (mmt) cc_final: 0.5509 (mmt) REVERT: B 809 ASP cc_start: 0.9384 (m-30) cc_final: 0.9183 (p0) REVERT: B 821 PHE cc_start: 0.8413 (t80) cc_final: 0.8096 (t80) REVERT: B 846 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8815 (mt-10) REVERT: B 852 MET cc_start: 0.8803 (ppp) cc_final: 0.8491 (ppp) REVERT: C 59 MET cc_start: 0.8082 (mmm) cc_final: 0.7455 (mmm) REVERT: C 69 MET cc_start: 0.6773 (mpp) cc_final: 0.5340 (tpt) REVERT: D 56 GLU cc_start: 0.7375 (mm-30) cc_final: 0.6694 (tp30) REVERT: D 69 MET cc_start: 0.4567 (mmm) cc_final: 0.3904 (tpp) REVERT: D 140 PHE cc_start: 0.7717 (m-80) cc_final: 0.6961 (m-80) REVERT: D 142 LYS cc_start: 0.4200 (mmtt) cc_final: 0.3447 (mmmt) REVERT: E 26 ILE cc_start: 0.8062 (mt) cc_final: 0.7600 (tt) REVERT: E 65 GLU cc_start: 0.6325 (tt0) cc_final: 0.5811 (tt0) REVERT: E 118 TYR cc_start: 0.7613 (t80) cc_final: 0.7292 (t80) REVERT: E 122 MET cc_start: 0.7970 (mtm) cc_final: 0.6819 (tpt) REVERT: F 20 MET cc_start: 0.4524 (ppp) cc_final: 0.0387 (mmm) REVERT: F 34 THR cc_start: 0.8218 (m) cc_final: 0.7542 (m) REVERT: F 40 ARG cc_start: 0.7053 (mmp-170) cc_final: 0.6654 (ptt-90) REVERT: F 69 MET cc_start: 0.0283 (mmt) cc_final: -0.0030 (mmm) outliers start: 33 outliers final: 28 residues processed: 232 average time/residue: 0.3005 time to fit residues: 107.5682 Evaluate side-chains 229 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 199 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 599 ASP Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 610 GLN Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 833 TYR Chi-restraints excluded: chain B residue 874 GLU Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 86 ASN Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain F residue 53 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 135 optimal weight: 1.9990 chunk 217 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 228 optimal weight: 6.9990 chunk 209 optimal weight: 0.8980 chunk 181 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 140 optimal weight: 0.9980 chunk 111 optimal weight: 0.0870 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 ASN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19205 Z= 0.167 Angle : 0.657 15.617 25854 Z= 0.324 Chirality : 0.041 0.221 2795 Planarity : 0.004 0.049 3346 Dihedral : 7.062 179.322 2534 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.53 % Allowed : 18.90 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.18), residues: 2283 helix: 0.68 (0.15), residues: 1294 sheet: -0.85 (0.40), residues: 153 loop : -0.77 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 816 HIS 0.005 0.001 HIS B 401 PHE 0.037 0.001 PHE B 621 TYR 0.017 0.001 TYR B 422 ARG 0.005 0.000 ARG A 858 ********************** 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 238 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 207 time to evaluate : 2.447 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: A 77 MET cc_start: 0.7768 (mmt) cc_final: 0.7299 (mmt) REVERT: A 113 MET cc_start: 0.6881 (mmt) cc_final: 0.6562 (mmt) REVERT: A 350 TYR cc_start: 0.8116 (m-80) cc_final: 0.7570 (m-80) REVERT: A 405 LYS cc_start: 0.9031 (ttmt) cc_final: 0.8782 (tttp) REVERT: A 410 TYR cc_start: 0.7450 (m-80) cc_final: 0.7133 (m-80) REVERT: A 865 LYS cc_start: 0.9328 (tppt) cc_final: 0.9024 (pttp) REVERT: B 43 LYS cc_start: 0.7910 (mmtp) cc_final: 0.7537 (mmmt) REVERT: B 113 MET cc_start: 0.7566 (mtp) cc_final: 0.7217 (mtm) REVERT: B 312 PHE cc_start: 0.6361 (m-10) cc_final: 0.6049 (m-10) REVERT: B 330 MET cc_start: 0.8201 (ppp) cc_final: 0.7986 (ptt) REVERT: B 435 MET cc_start: 0.8487 (tmm) cc_final: 0.7989 (tmm) REVERT: B 439 MET cc_start: 0.8252 (mtp) cc_final: 0.7963 (mtp) REVERT: B 447 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.6951 (mm) REVERT: B 536 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8588 (tm-30) REVERT: B 659 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8355 (mtm) REVERT: B 809 ASP cc_start: 0.9379 (m-30) cc_final: 0.9166 (p0) REVERT: B 821 PHE cc_start: 0.8392 (t80) cc_final: 0.8007 (t80) REVERT: B 846 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8799 (mt-10) REVERT: B 852 MET cc_start: 0.8749 (ppp) cc_final: 0.8338 (ppp) REVERT: B 874 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8434 (pp20) REVERT: C 59 MET cc_start: 0.8041 (mmm) cc_final: 0.7414 (mmm) REVERT: C 69 MET cc_start: 0.6802 (mpp) cc_final: 0.5384 (tpt) REVERT: C 102 GLU cc_start: 0.7479 (pm20) cc_final: 0.7272 (pm20) REVERT: D 56 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6557 (tp30) REVERT: D 69 MET cc_start: 0.4598 (mmm) cc_final: 0.4186 (tpp) REVERT: D 140 PHE cc_start: 0.7700 (m-80) cc_final: 0.6935 (m-80) REVERT: D 142 LYS cc_start: 0.4305 (mmtt) cc_final: 0.3559 (mmmt) REVERT: E 26 ILE cc_start: 0.8030 (mt) cc_final: 0.7584 (tt) REVERT: E 65 GLU cc_start: 0.6393 (tt0) cc_final: 0.5857 (tt0) REVERT: E 118 TYR cc_start: 0.7588 (t80) cc_final: 0.7266 (t80) REVERT: E 122 MET cc_start: 0.7965 (mtm) cc_final: 0.6830 (tpt) REVERT: F 20 MET cc_start: 0.4522 (ppp) cc_final: 0.0352 (mmm) REVERT: F 40 ARG cc_start: 0.7028 (mmp-170) cc_final: 0.6668 (ptt-90) REVERT: F 69 MET cc_start: 0.0301 (mmt) cc_final: -0.0382 (mmt) outliers start: 31 outliers final: 24 residues processed: 227 average time/residue: 0.3216 time to fit residues: 111.9518 Evaluate side-chains 230 residues out of total 2024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 203 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain B residue 31 PHE Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 515 MET Chi-restraints excluded: chain B residue 539 MET Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 833 TYR Chi-restraints excluded: chain B residue 874 GLU Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 86 ASN Chi-restraints excluded: chain D residue 117 MET Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain E residue 84 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 229 random chunks: chunk 144 optimal weight: 2.9990 chunk 193 optimal weight: 6.9990 chunk 55 optimal weight: 0.5980 chunk 167 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 50 optimal weight: 0.0770 chunk 181 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 186 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.1344 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 444 ASN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.076198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.060549 restraints weight = 163240.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.062323 restraints weight = 77246.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.063473 restraints weight = 47205.869| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 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 = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19205 Z= 0.190 Angle : 0.661 15.272 25854 Z= 0.325 Chirality : 0.041 0.222 2795 Planarity : 0.004 0.049 3346 Dihedral : 6.790 164.499 2534 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 18.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.63 % Allowed : 18.85 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.18), residues: 2283 helix: 0.69 (0.15), residues: 1290 sheet: -0.75 (0.41), residues: 148 loop : -0.72 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 816 HIS 0.005 0.001 HIS B 401 PHE 0.037 0.001 PHE E 86 TYR 0.019 0.001 TYR B 422 ARG 0.004 0.000 ARG A 858 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4364.64 seconds wall clock time: 80 minutes 9.63 seconds (4809.63 seconds total)