Starting phenix.real_space_refine on Wed Feb 14 23:49:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1z_30947/02_2024/7e1z_30947_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1z_30947/02_2024/7e1z_30947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1z_30947/02_2024/7e1z_30947.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1z_30947/02_2024/7e1z_30947.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1z_30947/02_2024/7e1z_30947_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e1z_30947/02_2024/7e1z_30947_neut.pdb" } resolution = 3.2 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= 0.005 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: 7 Type Number sf(0) Gaussians P 1 5.49 5 Mg 1 5.21 5 S 57 5.16 5 Na 4 4.78 5 C 6817 2.51 5 N 1714 2.21 5 O 1956 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 61": "NH1" <-> "NH2" Residue "A ARG 67": "NH1" <-> "NH2" Residue "A GLU 70": "OE1" <-> "OE2" Residue "A GLU 88": "OE1" <-> "OE2" Residue "A ARG 173": "NH1" <-> "NH2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A GLU 184": "OE1" <-> "OE2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ARG 471": "NH1" <-> "NH2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "A ARG 513": "NH1" <-> "NH2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A GLU 563": "OE1" <-> "OE2" Residue "A GLU 642": "OE1" <-> "OE2" Residue "A ARG 692": "NH1" <-> "NH2" Residue "A GLU 703": "OE1" <-> "OE2" Residue "A GLU 828": "OE1" <-> "OE2" Residue "A ARG 941": "NH1" <-> "NH2" Residue "A GLU 961": "OE1" <-> "OE2" Residue "A ARG 979": "NH1" <-> "NH2" Residue "A ARG 1011": "NH1" <-> "NH2" Residue "B ARG 27": "NH1" <-> "NH2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B ARG 91": "NH1" <-> "NH2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 171": "OE1" <-> "OE2" Residue "B TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 27": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10550 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 976, 7575 Classifications: {'peptide': 976} Link IDs: {'PTRANS': 43, 'TRANS': 932} Chain breaks: 1 Chain: "B" Number of atoms: 2404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2404 Classifications: {'peptide': 294} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 273} Chain: "C" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 256 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 199 Unusual residues: {' MG': 1, ' NA': 4, 'PC1': 1, 'Y01': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'NAG': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 6.58, per 1000 atoms: 0.62 Number of scatterers: 10550 At special positions: 0 Unit cell: (90.221, 96.743, 182.616, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 57 16.00 P 1 15.00 Mg 1 11.99 Na 4 11.00 O 1956 8.00 N 1714 7.00 C 6817 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS A 249 " distance=2.18 Simple disulfide: pdb=" SG CYS A 518 " - pdb=" SG CYS A 556 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 175 " distance=1.99 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 276 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG B 402 " - " ASN B 265 " " NAG D 1 " - " ASN B 158 " Time building additional restraints: 4.23 Conformation dependent library (CDL) restraints added in 2.0 seconds 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2410 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 13 sheets defined 44.2% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 89 through 97 removed outlier: 3.787A pdb=" N GLN A 95 " --> pdb=" O LYS A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 119 removed outlier: 3.807A pdb=" N ALA A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 159 removed outlier: 3.559A pdb=" N LEU A 132 " --> pdb=" O ASP A 128 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 154 " --> pdb=" O GLN A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 261 through 265 removed outlier: 4.007A pdb=" N ARG A 264 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR A 265 " --> pdb=" O GLY A 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 261 through 265' Processing helix chain 'A' and resid 284 through 311 removed outlier: 3.748A pdb=" N ILE A 288 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 314 No H-bonds generated for 'chain 'A' and resid 312 through 314' Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.990A pdb=" N THR A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR A 347 " --> pdb=" O CYS A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 363 through 368 removed outlier: 3.690A pdb=" N GLY A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 425 Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.731A pdb=" N LYS A 458 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N CYS A 459 " --> pdb=" O ALA A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 510 through 515 Processing helix chain 'A' and resid 531 through 547 Processing helix chain 'A' and resid 598 through 609 removed outlier: 3.607A pdb=" N ALA A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY A 604 " --> pdb=" O PRO A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 632 Processing helix chain 'A' and resid 640 through 649 Processing helix chain 'A' and resid 651 through 655 removed outlier: 3.707A pdb=" N GLN A 654 " --> pdb=" O PRO A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.506A pdb=" N LEU A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LYS A 683 " --> pdb=" O ASP A 679 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS A 685 " --> pdb=" O ILE A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 697 Processing helix chain 'A' and resid 698 through 707 removed outlier: 3.580A pdb=" N GLY A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 726 removed outlier: 3.824A pdb=" N LYS A 726 " --> pdb=" O SER A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 745 removed outlier: 3.647A pdb=" N ALA A 745 " --> pdb=" O VAL A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 780 removed outlier: 3.745A pdb=" N VAL A 759 " --> pdb=" O PHE A 755 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE A 768 " --> pdb=" O GLU A 764 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N PHE A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP A 770 " --> pdb=" O ARG A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 796 Proline residue: A 789 - end of helix Processing helix chain 'A' and resid 803 through 815 Processing helix chain 'A' and resid 820 through 825 removed outlier: 3.587A pdb=" N TYR A 824 " --> pdb=" O SER A 821 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU A 825 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 854 removed outlier: 3.692A pdb=" N ILE A 850 " --> pdb=" O ASN A 846 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET A 852 " --> pdb=" O ARG A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 877 removed outlier: 3.998A pdb=" N ILE A 860 " --> pdb=" O GLN A 856 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A 868 " --> pdb=" O GLY A 864 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY A 877 " --> pdb=" O LEU A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 884 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 907 through 937 removed outlier: 3.777A pdb=" N ARG A 911 " --> pdb=" O THR A 907 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 947 Processing helix chain 'A' and resid 951 through 970 removed outlier: 3.758A pdb=" N ILE A 955 " --> pdb=" O ASN A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 988 removed outlier: 3.826A pdb=" N TRP A 988 " --> pdb=" O PRO A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1011 Processing helix chain 'A' and resid 1015 through 1022 removed outlier: 3.551A pdb=" N TYR A1022 " --> pdb=" O GLU A1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 29 through 58 removed outlier: 3.518A pdb=" N PHE B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR B 39 " --> pdb=" O ILE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 113 through 117 removed outlier: 3.595A pdb=" N GLN B 117 " --> pdb=" O ASP B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 removed outlier: 3.636A pdb=" N TRP B 155 " --> pdb=" O LYS B 152 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY B 157 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.942A pdb=" N GLY B 172 " --> pdb=" O TYR B 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 46 removed outlier: 3.690A pdb=" N GLY C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 169 through 171 Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 193 removed outlier: 6.885A pdb=" N THR A 253 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ALA A 208 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG A 255 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASP A 202 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 203 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 212 through 214 Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 358 removed outlier: 6.214A pdb=" N VAL A 712 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL A 732 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL A 714 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N MET A 734 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR A 372 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N THR A 715 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N CYS A 374 " --> pdb=" O THR A 715 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE A 373 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL A 616 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER A 375 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL A 613 " --> pdb=" O ILE A 688 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N PHE A 690 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N MET A 615 " --> pdb=" O PHE A 690 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 387 through 388 removed outlier: 7.340A pdb=" N PHE A 555 " --> pdb=" O VAL A 586 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LEU A 588 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU A 553 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER A 590 " --> pdb=" O ARG A 551 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG A 551 " --> pdb=" O SER A 590 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A 509 " --> pdb=" O GLY A 554 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 432 through 433 removed outlier: 3.652A pdb=" N VAL A 432 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 478 through 479 removed outlier: 3.879A pdb=" N VAL A 478 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 521 through 522 Processing sheet with id=AA9, first strand: chain 'A' and resid 898 through 899 Processing sheet with id=AB1, first strand: chain 'B' and resid 23 through 24 Processing sheet with id=AB2, first strand: chain 'B' and resid 77 through 79 Processing sheet with id=AB3, first strand: chain 'B' and resid 87 through 90 removed outlier: 3.543A pdb=" N PHE B 90 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 123 through 124 412 hydrogen bonds defined for protein. 1164 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: 3.29 Time building geometry restraints manager: 4.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1743 1.31 - 1.43: 2704 1.43 - 1.56: 6187 1.56 - 1.69: 58 1.69 - 1.81: 84 Bond restraints: 10776 Sorted by residual: bond pdb=" CAI Y01 C1501 " pdb=" CAZ Y01 C1501 " ideal model delta sigma weight residual 1.332 1.553 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" CAI Y01 B 401 " pdb=" CAZ Y01 B 401 " ideal model delta sigma weight residual 1.332 1.551 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" CAI Y01 A1109 " pdb=" CAZ Y01 A1109 " ideal model delta sigma weight residual 1.332 1.551 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" CAI Y01 A1108 " pdb=" CAZ Y01 A1108 " ideal model delta sigma weight residual 1.332 1.550 -0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" CAI Y01 A1106 " pdb=" CAZ Y01 A1106 " ideal model delta sigma weight residual 1.332 1.550 -0.218 2.00e-02 2.50e+03 1.19e+02 ... (remaining 10771 not shown) Histogram of bond angle deviations from ideal: 99.51 - 107.20: 432 107.20 - 114.90: 6457 114.90 - 122.59: 6526 122.59 - 130.29: 1169 130.29 - 137.99: 43 Bond angle restraints: 14627 Sorted by residual: angle pdb=" N LYS A 727 " pdb=" CA LYS A 727 " pdb=" C LYS A 727 " ideal model delta sigma weight residual 114.62 105.90 8.72 1.14e+00 7.69e-01 5.85e+01 angle pdb=" O12 PC1 A1110 " pdb=" P PC1 A1110 " pdb=" O14 PC1 A1110 " ideal model delta sigma weight residual 123.67 101.06 22.61 3.00e+00 1.11e-01 5.68e+01 angle pdb=" N MET A 164 " pdb=" CA MET A 164 " pdb=" C MET A 164 " ideal model delta sigma weight residual 113.88 105.08 8.80 1.23e+00 6.61e-01 5.12e+01 angle pdb=" N GLN A 930 " pdb=" CA GLN A 930 " pdb=" C GLN A 930 " ideal model delta sigma weight residual 111.36 105.77 5.59 1.09e+00 8.42e-01 2.63e+01 angle pdb=" C CYS A 464 " pdb=" N GLY A 465 " pdb=" CA GLY A 465 " ideal model delta sigma weight residual 121.41 131.45 -10.04 1.96e+00 2.60e-01 2.62e+01 ... (remaining 14622 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 6455 35.40 - 70.80: 210 70.80 - 106.19: 53 106.19 - 141.59: 99 141.59 - 176.99: 18 Dihedral angle restraints: 6835 sinusoidal: 3083 harmonic: 3752 Sorted by residual: dihedral pdb=" CB CYS A 211 " pdb=" SG CYS A 211 " pdb=" SG CYS A 249 " pdb=" CB CYS A 249 " ideal model delta sinusoidal sigma weight residual -86.00 -174.72 88.72 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CA VAL B 72 " pdb=" C VAL B 72 " pdb=" N ALA B 73 " pdb=" CA ALA B 73 " ideal model delta harmonic sigma weight residual -180.00 -154.54 -25.46 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CB CYS B 159 " pdb=" SG CYS B 159 " pdb=" SG CYS B 175 " pdb=" CB CYS B 175 " ideal model delta sinusoidal sigma weight residual 93.00 133.23 -40.23 1 1.00e+01 1.00e-02 2.27e+01 ... (remaining 6832 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.197: 1629 1.197 - 2.394: 0 2.394 - 3.591: 0 3.591 - 4.789: 0 4.789 - 5.986: 30 Chirality restraints: 1659 Sorted by residual: chirality pdb=" CBI Y01 A1106 " pdb=" CAU Y01 A1106 " pdb=" CBE Y01 A1106 " pdb=" CBG Y01 A1106 " both_signs ideal model delta sigma weight residual False 2.94 -3.05 5.99 2.00e-01 2.50e+01 8.96e+02 chirality pdb=" CBI Y01 A1107 " pdb=" CAU Y01 A1107 " pdb=" CBE Y01 A1107 " pdb=" CBG Y01 A1107 " both_signs ideal model delta sigma weight residual False 2.94 -3.05 5.98 2.00e-01 2.50e+01 8.95e+02 chirality pdb=" CBI Y01 A1109 " pdb=" CAU Y01 A1109 " pdb=" CBE Y01 A1109 " pdb=" CBG Y01 A1109 " both_signs ideal model delta sigma weight residual False 2.94 -3.05 5.98 2.00e-01 2.50e+01 8.95e+02 ... (remaining 1656 not shown) Planarity restraints: 1844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 243 " -0.053 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO B 244 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 244 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 244 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 132 " 0.049 5.00e-02 4.00e+02 7.32e-02 8.56e+00 pdb=" N PRO B 133 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 133 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 133 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 163 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.02e+00 pdb=" C ASN B 163 " -0.046 2.00e-02 2.50e+03 pdb=" O ASN B 163 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP B 164 " 0.016 2.00e-02 2.50e+03 ... (remaining 1841 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 64 2.53 - 3.12: 7500 3.12 - 3.71: 15431 3.71 - 4.31: 22190 4.31 - 4.90: 37289 Nonbonded interactions: 82474 Sorted by model distance: nonbonded pdb=" O LEU A 63 " pdb=" OG1 THR A 64 " model vdw 1.934 2.440 nonbonded pdb=" OG SER B 11 " pdb=" N TRP B 12 " model vdw 2.189 2.520 nonbonded pdb=" CA GLY A 195 " pdb=" O VAL A 250 " model vdw 2.215 3.440 nonbonded pdb=" OG SER A 782 " pdb="NA NA A1103 " model vdw 2.220 2.470 nonbonded pdb=" CB ALA B 47 " pdb=" CAC Y01 B 401 " model vdw 2.226 3.880 ... (remaining 82469 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 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: 3.260 Check model and map are aligned: 0.160 Set scattering table: 0.120 Process input model: 31.770 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 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 : 0.013 0.221 10776 Z= 0.812 Angle : 1.206 22.611 14627 Z= 0.601 Chirality : 0.733 5.986 1659 Planarity : 0.007 0.080 1842 Dihedral : 28.018 176.991 4410 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 1.00 % Allowed : 6.72 % Favored : 92.27 % Rotamer: Outliers : 1.07 % Allowed : 8.49 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -3.99 (0.18), residues: 1294 helix: -2.69 (0.16), residues: 527 sheet: -1.94 (0.36), residues: 142 loop : -2.74 (0.21), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 890 HIS 0.006 0.001 HIS A 52 PHE 0.022 0.002 PHE B 295 TYR 0.021 0.002 TYR C 21 ARG 0.004 0.001 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 156 time to evaluate : 1.246 Fit side-chains revert: symmetry clash REVERT: A 46 LEU cc_start: 0.8730 (pp) cc_final: 0.8506 (pp) REVERT: A 48 LEU cc_start: 0.8025 (tt) cc_final: 0.7724 (mp) REVERT: A 117 ILE cc_start: 0.9122 (mt) cc_final: 0.8914 (mt) REVERT: A 212 LYS cc_start: 0.7652 (mptt) cc_final: 0.7300 (mtpp) REVERT: A 244 PHE cc_start: 0.7907 (m-80) cc_final: 0.7347 (m-10) REVERT: B 13 LYS cc_start: 0.4944 (OUTLIER) cc_final: 0.4653 (tppt) REVERT: B 51 ILE cc_start: 0.8902 (mm) cc_final: 0.8518 (mt) REVERT: B 80 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8185 (tp) outliers start: 12 outliers final: 5 residues processed: 166 average time/residue: 0.3107 time to fit residues: 67.6387 Evaluate side-chains 98 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 930 GLN Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 159 CYS Chi-restraints excluded: chain B residue 241 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.4980 chunk 97 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 117 optimal weight: 0.3980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 ASN A 248 ASN A 406 GLN ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 GLN A 503 HIS A 524 HIS A 540 ASN A 570 GLN A 744 GLN A 783 ASN A 882 HIS B 18 ASN B 69 GLN B 104 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10776 Z= 0.225 Angle : 1.620 34.802 14627 Z= 0.589 Chirality : 0.153 1.942 1659 Planarity : 0.005 0.046 1842 Dihedral : 31.669 179.019 1959 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.41 % Favored : 93.28 % Rotamer: Outliers : 2.06 % Allowed : 12.87 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.22), residues: 1294 helix: -0.68 (0.22), residues: 549 sheet: -1.69 (0.37), residues: 149 loop : -2.32 (0.23), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 89 HIS 0.005 0.001 HIS A 398 PHE 0.031 0.001 PHE A 870 TYR 0.018 0.001 TYR C 21 ARG 0.006 0.000 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 90 time to evaluate : 1.187 Fit side-chains revert: symmetry clash REVERT: A 126 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7817 (tm-30) REVERT: A 244 PHE cc_start: 0.7951 (m-80) cc_final: 0.7472 (m-10) REVERT: A 507 MET cc_start: 0.5626 (tpt) cc_final: 0.5367 (tpt) REVERT: A 513 ARG cc_start: 0.8283 (tpp80) cc_final: 0.7609 (mmp80) REVERT: A 592 ILE cc_start: 0.8902 (tp) cc_final: 0.8623 (tp) REVERT: A 933 ASP cc_start: 0.8534 (t0) cc_final: 0.8231 (t0) REVERT: B 80 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8366 (tp) REVERT: B 119 ASP cc_start: 0.7202 (t0) cc_final: 0.6966 (t0) outliers start: 23 outliers final: 9 residues processed: 109 average time/residue: 0.2373 time to fit residues: 36.9748 Evaluate side-chains 84 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 249 CYS Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain C residue 25 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 chunk 126 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 40 optimal weight: 20.0000 chunk 94 optimal weight: 5.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 GLN ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 HIS A 783 ASN A 896 ASN B 104 ASN B 141 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10776 Z= 0.330 Angle : 1.614 35.295 14627 Z= 0.590 Chirality : 0.154 1.864 1659 Planarity : 0.004 0.049 1842 Dihedral : 31.636 179.726 1941 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.72 % Favored : 93.04 % Rotamer: Outliers : 2.86 % Allowed : 13.32 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.23), residues: 1294 helix: 0.18 (0.23), residues: 525 sheet: -1.34 (0.40), residues: 134 loop : -1.97 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 89 HIS 0.003 0.001 HIS A 290 PHE 0.028 0.002 PHE A 870 TYR 0.019 0.001 TYR C 21 ARG 0.010 0.001 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 79 time to evaluate : 1.214 Fit side-chains REVERT: A 211 CYS cc_start: 0.6636 (OUTLIER) cc_final: 0.6326 (t) REVERT: A 244 PHE cc_start: 0.8003 (m-80) cc_final: 0.7467 (m-10) REVERT: A 507 MET cc_start: 0.5672 (tpt) cc_final: 0.5366 (tpt) REVERT: A 513 ARG cc_start: 0.8324 (tpp80) cc_final: 0.7698 (mmm-85) REVERT: A 591 MET cc_start: 0.8206 (ptp) cc_final: 0.7938 (ptp) REVERT: A 933 ASP cc_start: 0.8606 (t0) cc_final: 0.8335 (t0) REVERT: B 13 LYS cc_start: 0.5288 (OUTLIER) cc_final: 0.4858 (tppt) REVERT: B 20 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7836 (tm-30) REVERT: B 51 ILE cc_start: 0.8933 (mm) cc_final: 0.8599 (mt) REVERT: B 141 HIS cc_start: 0.6673 (OUTLIER) cc_final: 0.6447 (t-90) outliers start: 32 outliers final: 18 residues processed: 105 average time/residue: 0.2169 time to fit residues: 33.7865 Evaluate side-chains 91 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 70 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 44 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 33 optimal weight: 0.0000 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 GLN A 783 ASN B 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10776 Z= 0.149 Angle : 1.567 33.427 14627 Z= 0.560 Chirality : 0.156 1.883 1659 Planarity : 0.004 0.051 1842 Dihedral : 31.515 179.964 1941 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.03 % Favored : 93.82 % Rotamer: Outliers : 1.61 % Allowed : 15.82 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.94 (0.23), residues: 1294 helix: 0.72 (0.24), residues: 543 sheet: -1.16 (0.41), residues: 142 loop : -1.76 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 89 HIS 0.023 0.001 HIS B 141 PHE 0.021 0.001 PHE A 870 TYR 0.013 0.001 TYR C 21 ARG 0.006 0.000 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 1.323 Fit side-chains REVERT: A 122 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7001 (tp30) REVERT: A 126 GLN cc_start: 0.8385 (tm-30) cc_final: 0.7906 (tm-30) REVERT: A 164 MET cc_start: 0.7611 (tpt) cc_final: 0.7304 (tpp) REVERT: A 244 PHE cc_start: 0.7988 (m-80) cc_final: 0.7469 (m-10) REVERT: A 507 MET cc_start: 0.5706 (tpt) cc_final: 0.5429 (tpt) REVERT: A 711 ILE cc_start: 0.8262 (mm) cc_final: 0.8041 (mm) REVERT: A 748 MET cc_start: 0.8485 (ttm) cc_final: 0.8054 (ttp) REVERT: A 933 ASP cc_start: 0.8562 (t0) cc_final: 0.8273 (t0) REVERT: B 13 LYS cc_start: 0.4890 (OUTLIER) cc_final: 0.4547 (tppt) outliers start: 18 outliers final: 9 residues processed: 104 average time/residue: 0.1949 time to fit residues: 31.2523 Evaluate side-chains 88 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 294 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 GLN A 783 ASN A 905 GLN ** B 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10776 Z= 0.261 Angle : 1.589 34.275 14627 Z= 0.571 Chirality : 0.155 1.869 1659 Planarity : 0.004 0.052 1842 Dihedral : 31.428 179.858 1939 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.11 % Favored : 93.74 % Rotamer: Outliers : 2.14 % Allowed : 15.82 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.79 (0.24), residues: 1294 helix: 0.90 (0.24), residues: 538 sheet: -0.98 (0.42), residues: 142 loop : -1.75 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 89 HIS 0.002 0.001 HIS A 290 PHE 0.022 0.001 PHE A 870 TYR 0.017 0.001 TYR A 869 ARG 0.006 0.000 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 74 time to evaluate : 1.223 Fit side-chains REVERT: A 122 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7031 (tp30) REVERT: A 244 PHE cc_start: 0.8003 (m-80) cc_final: 0.7471 (m-10) REVERT: A 324 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8885 (tp) REVERT: A 507 MET cc_start: 0.5689 (tpt) cc_final: 0.5400 (tpt) REVERT: A 711 ILE cc_start: 0.8322 (mm) cc_final: 0.8093 (mm) REVERT: A 933 ASP cc_start: 0.8615 (t0) cc_final: 0.8352 (t0) REVERT: B 13 LYS cc_start: 0.5252 (OUTLIER) cc_final: 0.4816 (tppt) REVERT: B 51 ILE cc_start: 0.8937 (mm) cc_final: 0.8666 (mt) REVERT: B 202 MET cc_start: 0.7373 (pmm) cc_final: 0.6656 (ptt) outliers start: 24 outliers final: 17 residues processed: 95 average time/residue: 0.1928 time to fit residues: 28.4892 Evaluate side-chains 90 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 70 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain C residue 25 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 124 optimal weight: 0.0370 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 ASN B 141 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10776 Z= 0.145 Angle : 1.563 33.476 14627 Z= 0.556 Chirality : 0.157 1.892 1659 Planarity : 0.004 0.050 1842 Dihedral : 31.341 179.767 1939 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.95 % Favored : 93.97 % Rotamer: Outliers : 1.97 % Allowed : 16.35 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.39 (0.24), residues: 1294 helix: 1.29 (0.24), residues: 532 sheet: -0.76 (0.42), residues: 142 loop : -1.57 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 89 HIS 0.002 0.000 HIS A 290 PHE 0.021 0.001 PHE B 15 TYR 0.013 0.001 TYR C 21 ARG 0.005 0.000 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 78 time to evaluate : 1.196 Fit side-chains REVERT: A 122 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7063 (tp30) REVERT: A 244 PHE cc_start: 0.7987 (m-80) cc_final: 0.7461 (m-10) REVERT: A 324 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.9020 (tp) REVERT: A 492 ILE cc_start: 0.4739 (OUTLIER) cc_final: 0.4448 (tp) REVERT: A 507 MET cc_start: 0.5669 (tpt) cc_final: 0.5467 (tpt) REVERT: B 13 LYS cc_start: 0.5209 (OUTLIER) cc_final: 0.4849 (tppt) REVERT: B 202 MET cc_start: 0.7392 (pmm) cc_final: 0.6959 (ptt) outliers start: 22 outliers final: 14 residues processed: 96 average time/residue: 0.1916 time to fit residues: 28.4554 Evaluate side-chains 92 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 74 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain C residue 25 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 76 optimal weight: 0.0770 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 GLN ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 ASN B 141 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10776 Z= 0.225 Angle : 1.580 34.062 14627 Z= 0.566 Chirality : 0.156 1.889 1659 Planarity : 0.004 0.050 1842 Dihedral : 31.318 179.193 1939 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.41 % Favored : 93.43 % Rotamer: Outliers : 2.59 % Allowed : 16.44 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.24), residues: 1294 helix: 1.29 (0.24), residues: 538 sheet: -0.66 (0.43), residues: 142 loop : -1.60 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 89 HIS 0.002 0.000 HIS A 290 PHE 0.019 0.001 PHE A 870 TYR 0.016 0.001 TYR A 869 ARG 0.004 0.000 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 72 time to evaluate : 1.091 Fit side-chains REVERT: A 122 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7045 (tp30) REVERT: A 244 PHE cc_start: 0.8019 (m-80) cc_final: 0.7478 (m-10) REVERT: A 324 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8963 (tp) REVERT: A 492 ILE cc_start: 0.4617 (OUTLIER) cc_final: 0.4327 (tp) REVERT: A 504 LEU cc_start: 0.6392 (tt) cc_final: 0.6122 (tt) REVERT: A 507 MET cc_start: 0.5991 (tpt) cc_final: 0.5536 (tpt) REVERT: A 933 ASP cc_start: 0.8629 (t0) cc_final: 0.8349 (t0) REVERT: B 13 LYS cc_start: 0.5340 (OUTLIER) cc_final: 0.4882 (tppt) REVERT: B 51 ILE cc_start: 0.8930 (mm) cc_final: 0.8649 (mt) REVERT: B 202 MET cc_start: 0.7296 (pmm) cc_final: 0.6946 (ptt) outliers start: 29 outliers final: 20 residues processed: 97 average time/residue: 0.1914 time to fit residues: 28.9452 Evaluate side-chains 93 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 69 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain C residue 25 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 84 optimal weight: 0.5980 chunk 61 optimal weight: 0.0670 chunk 11 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 0.0070 overall best weight: 1.1340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 ASN B 141 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10776 Z= 0.161 Angle : 1.568 33.585 14627 Z= 0.558 Chirality : 0.157 1.891 1659 Planarity : 0.003 0.049 1842 Dihedral : 31.271 179.385 1939 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.11 % Favored : 93.82 % Rotamer: Outliers : 1.88 % Allowed : 17.25 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.15 (0.24), residues: 1294 helix: 1.47 (0.24), residues: 540 sheet: -0.48 (0.44), residues: 141 loop : -1.49 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 89 HIS 0.002 0.000 HIS A 290 PHE 0.023 0.001 PHE B 15 TYR 0.014 0.001 TYR C 20 ARG 0.004 0.000 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 77 time to evaluate : 1.372 Fit side-chains REVERT: A 122 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7190 (tp30) REVERT: A 244 PHE cc_start: 0.8025 (m-80) cc_final: 0.7478 (m-10) REVERT: A 324 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8997 (tp) REVERT: A 492 ILE cc_start: 0.4563 (OUTLIER) cc_final: 0.4270 (tp) REVERT: A 504 LEU cc_start: 0.6342 (tt) cc_final: 0.6088 (tt) REVERT: A 507 MET cc_start: 0.5881 (tpt) cc_final: 0.5465 (tpt) REVERT: A 591 MET cc_start: 0.8042 (ptp) cc_final: 0.7607 (ptp) REVERT: B 13 LYS cc_start: 0.5217 (OUTLIER) cc_final: 0.4794 (tppt) REVERT: B 125 ASP cc_start: 0.7760 (t0) cc_final: 0.7435 (t0) REVERT: B 202 MET cc_start: 0.7453 (pmm) cc_final: 0.7120 (ptt) outliers start: 21 outliers final: 16 residues processed: 95 average time/residue: 0.2077 time to fit residues: 30.4803 Evaluate side-chains 91 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 71 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain C residue 25 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 7.9990 chunk 115 optimal weight: 0.2980 chunk 119 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 chunk 50 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 ASN B 141 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10776 Z= 0.253 Angle : 1.587 34.111 14627 Z= 0.571 Chirality : 0.156 1.895 1659 Planarity : 0.004 0.049 1842 Dihedral : 31.259 179.670 1939 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.34 % Favored : 93.51 % Rotamer: Outliers : 2.32 % Allowed : 17.34 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.15 (0.24), residues: 1294 helix: 1.49 (0.24), residues: 532 sheet: -0.57 (0.42), residues: 147 loop : -1.46 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 89 HIS 0.002 0.000 HIS A 290 PHE 0.021 0.001 PHE B 15 TYR 0.016 0.001 TYR A 869 ARG 0.006 0.000 ARG B 118 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 71 time to evaluate : 1.204 Fit side-chains REVERT: A 122 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7034 (tp30) REVERT: A 244 PHE cc_start: 0.8051 (m-80) cc_final: 0.7484 (m-10) REVERT: A 324 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8923 (tp) REVERT: A 504 LEU cc_start: 0.6359 (tt) cc_final: 0.6098 (tt) REVERT: A 507 MET cc_start: 0.5923 (tpt) cc_final: 0.5527 (tpt) REVERT: A 933 ASP cc_start: 0.8636 (t0) cc_final: 0.8363 (t0) REVERT: B 13 LYS cc_start: 0.5204 (OUTLIER) cc_final: 0.4840 (tppt) REVERT: B 51 ILE cc_start: 0.8947 (mm) cc_final: 0.8655 (mt) REVERT: B 125 ASP cc_start: 0.7688 (t0) cc_final: 0.7391 (t0) REVERT: B 202 MET cc_start: 0.7408 (pmm) cc_final: 0.7067 (ptt) outliers start: 26 outliers final: 20 residues processed: 91 average time/residue: 0.1944 time to fit residues: 27.2530 Evaluate side-chains 91 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 68 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain C residue 25 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 118 optimal weight: 0.0770 chunk 102 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 79 optimal weight: 0.4980 chunk 62 optimal weight: 8.9990 chunk 81 optimal weight: 0.6980 chunk 109 optimal weight: 0.0970 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 ASN B 141 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10776 Z= 0.139 Angle : 1.563 33.379 14627 Z= 0.555 Chirality : 0.158 1.904 1659 Planarity : 0.004 0.049 1842 Dihedral : 31.201 179.886 1939 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.80 % Favored : 94.13 % Rotamer: Outliers : 1.61 % Allowed : 18.50 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.08 (0.24), residues: 1294 helix: 1.65 (0.24), residues: 538 sheet: -0.40 (0.43), residues: 147 loop : -1.35 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 89 HIS 0.002 0.000 HIS A 503 PHE 0.019 0.001 PHE B 15 TYR 0.012 0.001 TYR A 869 ARG 0.006 0.000 ARG B 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 75 time to evaluate : 1.379 Fit side-chains REVERT: A 126 GLN cc_start: 0.8432 (tm-30) cc_final: 0.8029 (tm-30) REVERT: A 244 PHE cc_start: 0.8030 (m-80) cc_final: 0.7455 (m-10) REVERT: A 324 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8998 (tp) REVERT: A 591 MET cc_start: 0.8027 (ptp) cc_final: 0.7638 (ptp) REVERT: B 125 ASP cc_start: 0.7713 (t0) cc_final: 0.7393 (t0) REVERT: B 202 MET cc_start: 0.7539 (pmm) cc_final: 0.7087 (ptt) outliers start: 18 outliers final: 14 residues processed: 90 average time/residue: 0.1895 time to fit residues: 26.3752 Evaluate side-chains 84 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 69 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 294 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 chunk 15 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 102 optimal weight: 0.0170 chunk 42 optimal weight: 8.9990 chunk 105 optimal weight: 0.1980 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 GLN B 141 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.131664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.088802 restraints weight = 18335.996| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.56 r_work: 0.2936 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10776 Z= 0.140 Angle : 1.561 33.443 14627 Z= 0.554 Chirality : 0.157 1.904 1659 Planarity : 0.004 0.049 1842 Dihedral : 31.170 179.935 1939 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.72 % Favored : 94.20 % Rotamer: Outliers : 1.34 % Allowed : 18.77 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.15 (0.24), residues: 1294 helix: 1.71 (0.24), residues: 538 sheet: -0.30 (0.43), residues: 147 loop : -1.32 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 89 HIS 0.001 0.000 HIS A 290 PHE 0.032 0.001 PHE B 15 TYR 0.013 0.001 TYR A 869 ARG 0.008 0.000 ARG B 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2188.66 seconds wall clock time: 40 minutes 39.89 seconds (2439.89 seconds total)