Starting phenix.real_space_refine on Mon May 19 04:51:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pr3_17833/05_2025/8pr3_17833.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pr3_17833/05_2025/8pr3_17833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pr3_17833/05_2025/8pr3_17833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pr3_17833/05_2025/8pr3_17833.map" model { file = "/net/cci-nas-00/data/ceres_data/8pr3_17833/05_2025/8pr3_17833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pr3_17833/05_2025/8pr3_17833.cif" } resolution = 3.9 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= 0.001 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 11319 2.51 5 N 3146 2.21 5 O 3351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17888 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 880 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 1, 'TRANS': 103} Chain: "C" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 886 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain: "f" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3449 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 12, 'TRANS': 407} Chain breaks: 1 Chain: "h" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2897 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 17, 'TRANS': 353} Chain: "j" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2428 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 12, 'TRANS': 286} Chain breaks: 1 Chain: "m" Number of atoms: 4321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4321 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 13, 'TRANS': 509} Chain breaks: 3 Chain: "o" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2897 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 17, 'TRANS': 353} Chain: "E" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 65 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 65 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 10.01, per 1000 atoms: 0.56 Number of scatterers: 17888 At special positions: 0 Unit cell: (119.667, 124.962, 173.676, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 3351 8.00 N 3146 7.00 C 11319 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 - 3.00 Amino acid : True - 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: 4.13 Conformation dependent library (CDL) restraints added in 2.1 seconds 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4240 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 17 sheets defined 51.9% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'B' and resid 26 through 47 Processing helix chain 'B' and resid 55 through 128 removed outlier: 3.626A pdb=" N ASN B 61 " --> pdb=" O PRO B 57 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 78 " --> pdb=" O GLN B 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 47 Processing helix chain 'C' and resid 55 through 128 removed outlier: 3.873A pdb=" N ASN C 61 " --> pdb=" O PRO C 57 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL C 62 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR C 92 " --> pdb=" O GLU C 88 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS C 107 " --> pdb=" O GLN C 103 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE C 109 " --> pdb=" O GLU C 105 " (cutoff:3.500A) Processing helix chain 'f' and resid 561 through 572 Processing helix chain 'f' and resid 577 through 586 Processing helix chain 'f' and resid 588 through 592 removed outlier: 3.578A pdb=" N LEU f 591 " --> pdb=" O PHE f 588 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE f 592 " --> pdb=" O ASN f 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 588 through 592' Processing helix chain 'f' and resid 596 through 604 removed outlier: 4.267A pdb=" N ALA f 600 " --> pdb=" O HIS f 596 " (cutoff:3.500A) Processing helix chain 'f' and resid 604 through 625 removed outlier: 4.060A pdb=" N VAL f 625 " --> pdb=" O ASP f 621 " (cutoff:3.500A) Processing helix chain 'f' and resid 630 through 637 removed outlier: 3.768A pdb=" N LYS f 634 " --> pdb=" O SER f 630 " (cutoff:3.500A) Processing helix chain 'f' and resid 642 through 670 Processing helix chain 'f' and resid 676 through 691 Processing helix chain 'f' and resid 692 through 694 No H-bonds generated for 'chain 'f' and resid 692 through 694' Processing helix chain 'f' and resid 695 through 710 removed outlier: 3.509A pdb=" N PHE f 699 " --> pdb=" O THR f 695 " (cutoff:3.500A) Processing helix chain 'f' and resid 740 through 754 removed outlier: 3.765A pdb=" N ILE f 744 " --> pdb=" O LEU f 740 " (cutoff:3.500A) Processing helix chain 'f' and resid 761 through 773 Processing helix chain 'f' and resid 774 through 798 removed outlier: 3.571A pdb=" N ALA f 778 " --> pdb=" O LEU f 774 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER f 780 " --> pdb=" O PRO f 776 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG f 798 " --> pdb=" O LYS f 794 " (cutoff:3.500A) Processing helix chain 'f' and resid 799 through 804 removed outlier: 3.740A pdb=" N SER f 802 " --> pdb=" O ASN f 799 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LEU f 803 " --> pdb=" O THR f 800 " (cutoff:3.500A) Processing helix chain 'f' and resid 805 through 820 Processing helix chain 'f' and resid 828 through 863 removed outlier: 3.665A pdb=" N TYR f 832 " --> pdb=" O LYS f 828 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL f 833 " --> pdb=" O LEU f 829 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN f 834 " --> pdb=" O ASP f 830 " (cutoff:3.500A) Processing helix chain 'f' and resid 870 through 891 removed outlier: 3.705A pdb=" N HIS f 891 " --> pdb=" O ASP f 887 " (cutoff:3.500A) Processing helix chain 'f' and resid 895 through 923 removed outlier: 3.661A pdb=" N GLU f 906 " --> pdb=" O LYS f 902 " (cutoff:3.500A) Processing helix chain 'f' and resid 986 through 995 removed outlier: 3.926A pdb=" N LYS f 990 " --> pdb=" O MET f 986 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET f 991 " --> pdb=" O PHE f 987 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL f 992 " --> pdb=" O ALA f 988 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL f 993 " --> pdb=" O TRP f 989 " (cutoff:3.500A) Processing helix chain 'f' and resid 1013 through 1018 Processing helix chain 'f' and resid 1030 through 1039 removed outlier: 3.889A pdb=" N ALA f1039 " --> pdb=" O GLU f1035 " (cutoff:3.500A) Processing helix chain 'h' and resid 574 through 579 Processing helix chain 'h' and resid 583 through 608 removed outlier: 3.917A pdb=" N GLU h 603 " --> pdb=" O ARG h 599 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU h 604 " --> pdb=" O ALA h 600 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU h 605 " --> pdb=" O ASP h 601 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA h 606 " --> pdb=" O ALA h 602 " (cutoff:3.500A) Processing helix chain 'j' and resid 66 through 76 removed outlier: 3.674A pdb=" N LYS j 73 " --> pdb=" O THR j 69 " (cutoff:3.500A) Processing helix chain 'j' and resid 112 through 117 removed outlier: 4.691A pdb=" N GLY j 117 " --> pdb=" O TYR j 114 " (cutoff:3.500A) Processing helix chain 'j' and resid 118 through 123 removed outlier: 3.654A pdb=" N ALA j 122 " --> pdb=" O LEU j 118 " (cutoff:3.500A) Processing helix chain 'j' and resid 141 through 143 No H-bonds generated for 'chain 'j' and resid 141 through 143' Processing helix chain 'j' and resid 144 through 161 removed outlier: 4.241A pdb=" N SER j 148 " --> pdb=" O THR j 144 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP j 161 " --> pdb=" O ARG j 157 " (cutoff:3.500A) Processing helix chain 'j' and resid 168 through 183 Processing helix chain 'j' and resid 233 through 236 Processing helix chain 'j' and resid 237 through 243 removed outlier: 3.566A pdb=" N GLU j 243 " --> pdb=" O VAL j 239 " (cutoff:3.500A) Processing helix chain 'j' and resid 247 through 266 removed outlier: 3.517A pdb=" N HIS j 257 " --> pdb=" O PHE j 253 " (cutoff:3.500A) Processing helix chain 'j' and resid 279 through 293 Processing helix chain 'j' and resid 320 through 325 removed outlier: 3.798A pdb=" N GLU j 325 " --> pdb=" O ILE j 322 " (cutoff:3.500A) Processing helix chain 'j' and resid 358 through 373 removed outlier: 3.694A pdb=" N GLN j 373 " --> pdb=" O LEU j 369 " (cutoff:3.500A) Processing helix chain 'm' and resid 270 through 287 removed outlier: 3.697A pdb=" N GLU m 274 " --> pdb=" O THR m 270 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU m 282 " --> pdb=" O TRP m 278 " (cutoff:3.500A) Processing helix chain 'm' and resid 323 through 337 Proline residue: m 334 - end of helix Processing helix chain 'm' and resid 340 through 347 removed outlier: 4.005A pdb=" N LEU m 344 " --> pdb=" O PRO m 340 " (cutoff:3.500A) Processing helix chain 'm' and resid 349 through 364 Processing helix chain 'm' and resid 373 through 400 Processing helix chain 'm' and resid 401 through 404 removed outlier: 3.506A pdb=" N VAL m 404 " --> pdb=" O LEU m 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 401 through 404' Processing helix chain 'm' and resid 405 through 439 removed outlier: 3.508A pdb=" N PHE m 409 " --> pdb=" O ALA m 405 " (cutoff:3.500A) Processing helix chain 'm' and resid 456 through 484 removed outlier: 5.392A pdb=" N GLN m 472 " --> pdb=" O LYS m 468 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL m 479 " --> pdb=" O GLN m 475 " (cutoff:3.500A) Processing helix chain 'm' and resid 514 through 532 Processing helix chain 'm' and resid 539 through 569 Processing helix chain 'm' and resid 570 through 575 Processing helix chain 'm' and resid 577 through 588 Processing helix chain 'm' and resid 589 through 593 removed outlier: 3.825A pdb=" N VAL m 593 " --> pdb=" O ALA m 590 " (cutoff:3.500A) Processing helix chain 'm' and resid 594 through 601 removed outlier: 3.575A pdb=" N ILE m 601 " --> pdb=" O ILE m 597 " (cutoff:3.500A) Processing helix chain 'm' and resid 602 through 623 removed outlier: 3.702A pdb=" N THR m 606 " --> pdb=" O ARG m 602 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLN m 607 " --> pdb=" O GLU m 603 " (cutoff:3.500A) Processing helix chain 'm' and resid 630 through 638 removed outlier: 4.183A pdb=" N LYS m 634 " --> pdb=" O SER m 630 " (cutoff:3.500A) Processing helix chain 'm' and resid 642 through 670 Processing helix chain 'm' and resid 672 through 676 Processing helix chain 'm' and resid 678 through 693 removed outlier: 3.585A pdb=" N LEU m 682 " --> pdb=" O GLU m 678 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS m 692 " --> pdb=" O SER m 688 " (cutoff:3.500A) Processing helix chain 'm' and resid 695 through 710 removed outlier: 3.504A pdb=" N PHE m 699 " --> pdb=" O THR m 695 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN m 710 " --> pdb=" O VAL m 706 " (cutoff:3.500A) Processing helix chain 'm' and resid 742 through 754 removed outlier: 4.156A pdb=" N LEU m 746 " --> pdb=" O GLU m 742 " (cutoff:3.500A) Processing helix chain 'm' and resid 761 through 798 Proline residue: m 776 - end of helix Processing helix chain 'm' and resid 799 through 802 removed outlier: 3.517A pdb=" N SER m 802 " --> pdb=" O ASN m 799 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 799 through 802' Processing helix chain 'm' and resid 805 through 821 removed outlier: 3.628A pdb=" N LYS m 809 " --> pdb=" O VAL m 805 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS m 810 " --> pdb=" O ALA m 806 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU m 811 " --> pdb=" O GLY m 807 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA m 821 " --> pdb=" O ALA m 817 " (cutoff:3.500A) Processing helix chain 'm' and resid 828 through 854 removed outlier: 3.571A pdb=" N TYR m 832 " --> pdb=" O LYS m 828 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLN m 834 " --> pdb=" O ASP m 830 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR m 839 " --> pdb=" O ARG m 835 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE m 852 " --> pdb=" O ASP m 848 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE m 853 " --> pdb=" O ASP m 849 " (cutoff:3.500A) Processing helix chain 'o' and resid 574 through 579 removed outlier: 3.553A pdb=" N VAL o 579 " --> pdb=" O GLU o 575 " (cutoff:3.500A) Processing helix chain 'o' and resid 583 through 608 removed outlier: 4.500A pdb=" N ALA o 593 " --> pdb=" O GLY o 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 439 Processing helix chain 'F' and resid 430 through 439 removed outlier: 3.565A pdb=" N LYS F 439 " --> pdb=" O SER F 435 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'f' and resid 718 through 723 Processing sheet with id=AA2, first strand: chain 'h' and resid 239 through 245 removed outlier: 5.463A pdb=" N LEU h 241 " --> pdb=" O ASP h 572 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ASP h 572 " --> pdb=" O LEU h 241 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'h' and resid 256 through 261 removed outlier: 4.345A pdb=" N CYS h 258 " --> pdb=" O SER h 272 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL h 286 " --> pdb=" O TYR h 273 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY h 285 " --> pdb=" O CYS h 305 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'h' and resid 309 through 314 Processing sheet with id=AA5, first strand: chain 'h' and resid 358 through 365 removed outlier: 3.915A pdb=" N CYS h 360 " --> pdb=" O ILE h 375 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LYS h 380 " --> pdb=" O SER h 376 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP h 394 " --> pdb=" O SER h 383 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'h' and resid 408 through 412 removed outlier: 6.876A pdb=" N GLY h 424 " --> pdb=" O THR h 409 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N MET h 411 " --> pdb=" O VAL h 422 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL h 422 " --> pdb=" O MET h 411 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL h 430 " --> pdb=" O MET h 445 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N MET h 445 " --> pdb=" O VAL h 430 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR h 432 " --> pdb=" O SER h 443 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'h' and resid 453 through 458 removed outlier: 3.557A pdb=" N PHE h 471 " --> pdb=" O TRP h 483 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR h 492 " --> pdb=" O LEU h 482 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'h' and resid 501 through 506 removed outlier: 4.975A pdb=" N ASP h 503 " --> pdb=" O VAL h 517 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL h 517 " --> pdb=" O ASP h 503 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET h 505 " --> pdb=" O ALA h 515 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA h 515 " --> pdb=" O MET h 505 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP h 518 " --> pdb=" O ARG h 522 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ARG h 522 " --> pdb=" O ASP h 518 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA h 537 " --> pdb=" O LEU h 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'j' and resid 86 through 94 removed outlier: 6.061A pdb=" N ASN j 56 " --> pdb=" O LEU j 132 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ILE j 134 " --> pdb=" O ASN j 56 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N LEU j 58 " --> pdb=" O ILE j 134 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL j 136 " --> pdb=" O LEU j 58 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE j 60 " --> pdb=" O VAL j 136 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ASP j 138 " --> pdb=" O PHE j 60 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE j 270 " --> pdb=" O VAL j 229 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'o' and resid 239 through 245 removed outlier: 3.651A pdb=" N SER o 240 " --> pdb=" O ASP o 572 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ILE o 570 " --> pdb=" O ASN o 242 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLN o 244 " --> pdb=" O ILE o 568 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE o 568 " --> pdb=" O GLN o 244 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'o' and resid 256 through 261 removed outlier: 6.272A pdb=" N SER o 272 " --> pdb=" O SER o 257 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU o 259 " --> pdb=" O VAL o 270 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL o 270 " --> pdb=" O LEU o 259 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TRP o 261 " --> pdb=" O LEU o 268 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU o 268 " --> pdb=" O TRP o 261 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU o 288 " --> pdb=" O ALA o 271 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL o 286 " --> pdb=" O TYR o 273 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR o 301 " --> pdb=" O VAL o 289 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'o' and resid 309 through 314 Processing sheet with id=AB4, first strand: chain 'o' and resid 358 through 365 removed outlier: 3.871A pdb=" N CYS o 360 " --> pdb=" O ILE o 375 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS o 380 " --> pdb=" O SER o 376 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'o' and resid 399 through 400 Processing sheet with id=AB6, first strand: chain 'o' and resid 411 through 412 removed outlier: 7.016A pdb=" N VAL o 430 " --> pdb=" O MET o 445 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N MET o 445 " --> pdb=" O VAL o 430 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR o 432 " --> pdb=" O SER o 443 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'o' and resid 453 through 458 removed outlier: 3.591A pdb=" N TYR o 492 " --> pdb=" O LEU o 482 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'o' and resid 501 through 506 removed outlier: 6.865A pdb=" N VAL o 517 " --> pdb=" O TYR o 502 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL o 504 " --> pdb=" O ALA o 515 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALA o 515 " --> pdb=" O VAL o 504 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N TRP o 506 " --> pdb=" O LEU o 513 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU o 513 " --> pdb=" O TRP o 506 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP o 518 " --> pdb=" O ARG o 522 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ARG o 522 " --> pdb=" O ASP o 518 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA o 537 " --> pdb=" O LEU o 525 " (cutoff:3.500A) 978 hydrogen bonds defined for protein. 2877 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: 5.93 Time building geometry restraints manager: 4.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5769 1.34 - 1.46: 4115 1.46 - 1.58: 8247 1.58 - 1.71: 1 1.71 - 1.83: 118 Bond restraints: 18250 Sorted by residual: bond pdb=" C ILE m 601 " pdb=" N ARG m 602 " ideal model delta sigma weight residual 1.332 1.296 0.036 1.40e-02 5.10e+03 6.73e+00 bond pdb=" N SER E 438 " pdb=" CA SER E 438 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.31e-02 5.83e+03 5.90e+00 bond pdb=" CB GLU B 121 " pdb=" CG GLU B 121 " ideal model delta sigma weight residual 1.520 1.585 -0.065 3.00e-02 1.11e+03 4.70e+00 bond pdb=" CB GLN f 610 " pdb=" CG GLN f 610 " ideal model delta sigma weight residual 1.520 1.583 -0.063 3.00e-02 1.11e+03 4.35e+00 bond pdb=" CB GLN f 605 " pdb=" CG GLN f 605 " ideal model delta sigma weight residual 1.520 1.577 -0.057 3.00e-02 1.11e+03 3.65e+00 ... (remaining 18245 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.40: 24438 4.40 - 8.80: 205 8.80 - 13.20: 37 13.20 - 17.60: 8 17.60 - 22.00: 3 Bond angle restraints: 24691 Sorted by residual: angle pdb=" CB MET f 662 " pdb=" CG MET f 662 " pdb=" SD MET f 662 " ideal model delta sigma weight residual 112.70 131.58 -18.88 3.00e+00 1.11e-01 3.96e+01 angle pdb=" CA LEU m 357 " pdb=" CB LEU m 357 " pdb=" CG LEU m 357 " ideal model delta sigma weight residual 116.30 138.30 -22.00 3.50e+00 8.16e-02 3.95e+01 angle pdb=" CA LEU m 393 " pdb=" CB LEU m 393 " pdb=" CG LEU m 393 " ideal model delta sigma weight residual 116.30 138.02 -21.72 3.50e+00 8.16e-02 3.85e+01 angle pdb=" N LEU E 437 " pdb=" CA LEU E 437 " pdb=" C LEU E 437 " ideal model delta sigma weight residual 111.14 117.74 -6.60 1.08e+00 8.57e-01 3.73e+01 angle pdb=" N ASN F 434 " pdb=" CA ASN F 434 " pdb=" C ASN F 434 " ideal model delta sigma weight residual 111.36 105.38 5.98 1.09e+00 8.42e-01 3.01e+01 ... (remaining 24686 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 9299 17.81 - 35.62: 1325 35.62 - 53.42: 312 53.42 - 71.23: 70 71.23 - 89.04: 29 Dihedral angle restraints: 11035 sinusoidal: 4522 harmonic: 6513 Sorted by residual: dihedral pdb=" CA PHE m 339 " pdb=" C PHE m 339 " pdb=" N PRO m 340 " pdb=" CA PRO m 340 " ideal model delta harmonic sigma weight residual -180.00 -155.52 -24.48 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA MET o 445 " pdb=" C MET o 445 " pdb=" N PHE o 446 " pdb=" CA PHE o 446 " ideal model delta harmonic sigma weight residual 180.00 157.40 22.60 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA GLU o 444 " pdb=" C GLU o 444 " pdb=" N MET o 445 " pdb=" CA MET o 445 " ideal model delta harmonic sigma weight residual 180.00 158.08 21.92 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 11032 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1960 0.052 - 0.103: 601 0.103 - 0.155: 133 0.155 - 0.206: 34 0.206 - 0.258: 7 Chirality restraints: 2735 Sorted by residual: chirality pdb=" CB ILE j 134 " pdb=" CA ILE j 134 " pdb=" CG1 ILE j 134 " pdb=" CG2 ILE j 134 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB ILE m 698 " pdb=" CA ILE m 698 " pdb=" CG1 ILE m 698 " pdb=" CG2 ILE m 698 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CB VAL m 381 " pdb=" CA VAL m 381 " pdb=" CG1 VAL m 381 " pdb=" CG2 VAL m 381 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 2732 not shown) Planarity restraints: 3192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE m 339 " -0.041 2.00e-02 2.50e+03 8.06e-02 6.49e+01 pdb=" C PHE m 339 " 0.139 2.00e-02 2.50e+03 pdb=" O PHE m 339 " -0.052 2.00e-02 2.50e+03 pdb=" N PRO m 340 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG f1003 " -0.291 9.50e-02 1.11e+02 1.31e-01 1.05e+01 pdb=" NE ARG f1003 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG f1003 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG f1003 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG f1003 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP f 849 " 0.015 2.00e-02 2.50e+03 2.92e-02 8.56e+00 pdb=" CG ASP f 849 " -0.051 2.00e-02 2.50e+03 pdb=" OD1 ASP f 849 " 0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP f 849 " 0.017 2.00e-02 2.50e+03 ... (remaining 3189 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4967 2.80 - 3.33: 16656 3.33 - 3.85: 31462 3.85 - 4.38: 33640 4.38 - 4.90: 57977 Nonbonded interactions: 144702 Sorted by model distance: nonbonded pdb=" OG SER h 475 " pdb=" OD1 ASP h 477 " model vdw 2.278 3.040 nonbonded pdb=" OG1 THR h 454 " pdb=" O TYR h 502 " model vdw 2.307 3.040 nonbonded pdb=" O ILE j 287 " pdb=" OG1 THR j 291 " model vdw 2.309 3.040 nonbonded pdb=" O GLU m 783 " pdb=" OG1 THR m 787 " model vdw 2.310 3.040 nonbonded pdb=" O SER j 127 " pdb=" OG1 THR j 131 " model vdw 2.314 3.040 ... (remaining 144697 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'C' and resid 24 through 128) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'h' selection = chain 'o' } 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 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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.740 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 38.700 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 18250 Z= 0.268 Angle : 1.079 22.004 24691 Z= 0.544 Chirality : 0.054 0.258 2735 Planarity : 0.006 0.131 3192 Dihedral : 17.802 89.039 6795 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.01 % Favored : 96.94 % Rotamer: Outliers : 0.67 % Allowed : 26.56 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.16), residues: 2193 helix: -0.49 (0.14), residues: 1061 sheet: -0.84 (0.28), residues: 335 loop : -0.95 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP h 552 HIS 0.011 0.001 HIS o 400 PHE 0.033 0.002 PHE m 843 TYR 0.022 0.002 TYR h 301 ARG 0.015 0.001 ARG f1020 Details of bonding type rmsd hydrogen bonds : bond 0.15997 ( 978) hydrogen bonds : angle 6.54056 ( 2877) covalent geometry : bond 0.00590 (18250) covalent geometry : angle 1.07887 (24691) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 216 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 ARG cc_start: 0.8118 (ttp80) cc_final: 0.7823 (ttp80) REVERT: B 122 LEU cc_start: 0.9081 (mt) cc_final: 0.8615 (tp) REVERT: C 98 LYS cc_start: 0.9217 (ttmm) cc_final: 0.8906 (ttmm) REVERT: C 103 GLN cc_start: 0.9203 (mm-40) cc_final: 0.8957 (pp30) REVERT: C 123 GLN cc_start: 0.9051 (tp-100) cc_final: 0.8792 (tp-100) REVERT: j 103 ARG cc_start: 0.8329 (mmp-170) cc_final: 0.7784 (mmm160) REVERT: o 310 MET cc_start: 0.8528 (ptp) cc_final: 0.8293 (ptp) REVERT: o 400 HIS cc_start: 0.7132 (OUTLIER) cc_final: 0.6458 (t-90) outliers start: 13 outliers final: 8 residues processed: 226 average time/residue: 0.3381 time to fit residues: 110.3243 Evaluate side-chains 197 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 188 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain f residue 713 VAL Chi-restraints excluded: chain f residue 755 TRP Chi-restraints excluded: chain f residue 993 VAL Chi-restraints excluded: chain j residue 239 VAL Chi-restraints excluded: chain m residue 576 LYS Chi-restraints excluded: chain o residue 381 ILE Chi-restraints excluded: chain o residue 400 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 184 optimal weight: 10.0000 chunk 165 optimal weight: 0.0370 chunk 92 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 111 optimal weight: 10.0000 chunk 88 optimal weight: 0.7980 chunk 171 optimal weight: 3.9990 chunk 66 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 198 optimal weight: 3.9990 overall best weight: 1.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 916 GLN ** h 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 373 GLN ** m 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 469 HIS ** o 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.080801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.058621 restraints weight = 69872.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.060499 restraints weight = 35854.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.061694 restraints weight = 23594.041| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18250 Z= 0.157 Angle : 0.614 11.206 24691 Z= 0.316 Chirality : 0.041 0.145 2735 Planarity : 0.004 0.049 3192 Dihedral : 4.836 46.606 2426 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.33 % Favored : 97.63 % Rotamer: Outliers : 2.26 % Allowed : 23.78 % Favored : 73.96 % 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: 0.27 (0.18), residues: 2193 helix: 1.05 (0.16), residues: 1067 sheet: -0.77 (0.26), residues: 383 loop : -0.41 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP j 143 HIS 0.004 0.001 HIS m 473 PHE 0.014 0.001 PHE m 843 TYR 0.014 0.001 TYR o 502 ARG 0.004 0.000 ARG j 103 Details of bonding type rmsd hydrogen bonds : bond 0.04595 ( 978) hydrogen bonds : angle 4.62412 ( 2877) covalent geometry : bond 0.00332 (18250) covalent geometry : angle 0.61376 (24691) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 199 time to evaluate : 1.929 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: B 107 LYS cc_start: 0.9363 (tmmt) cc_final: 0.9016 (tptt) REVERT: C 123 GLN cc_start: 0.9037 (tp-100) cc_final: 0.8785 (tp-100) REVERT: f 605 GLN cc_start: 0.8046 (tm-30) cc_final: 0.7739 (tm-30) REVERT: f 610 GLN cc_start: 0.8318 (tp40) cc_final: 0.8076 (tp40) REVERT: f 991 MET cc_start: 0.8362 (ptp) cc_final: 0.7961 (ptp) REVERT: f 1026 MET cc_start: 0.8000 (mmm) cc_final: 0.7160 (tpp) REVERT: j 126 GLU cc_start: 0.9007 (pp20) cc_final: 0.8806 (pp20) REVERT: j 162 LYS cc_start: 0.8741 (mttt) cc_final: 0.8515 (mtpt) REVERT: j 163 MET cc_start: 0.6919 (pmm) cc_final: 0.6666 (pmm) REVERT: m 413 MET cc_start: 0.9153 (ppp) cc_final: 0.8850 (ppp) REVERT: m 846 LYS cc_start: 0.8869 (mmtm) cc_final: 0.8607 (mmtm) REVERT: o 400 HIS cc_start: 0.6991 (OUTLIER) cc_final: 0.6298 (t70) REVERT: o 567 GLN cc_start: 0.8551 (pm20) cc_final: 0.8322 (pm20) outliers start: 44 outliers final: 31 residues processed: 233 average time/residue: 0.3198 time to fit residues: 110.7538 Evaluate side-chains 205 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain f residue 713 VAL Chi-restraints excluded: chain f residue 746 LEU Chi-restraints excluded: chain f residue 845 GLU Chi-restraints excluded: chain f residue 993 VAL Chi-restraints excluded: chain h residue 381 ILE Chi-restraints excluded: chain h residue 396 MET Chi-restraints excluded: chain h residue 411 MET Chi-restraints excluded: chain h residue 550 VAL Chi-restraints excluded: chain j residue 123 VAL Chi-restraints excluded: chain j residue 156 LEU Chi-restraints excluded: chain j residue 239 VAL Chi-restraints excluded: chain j residue 258 LEU Chi-restraints excluded: chain m residue 339 PHE Chi-restraints excluded: chain m residue 576 LYS Chi-restraints excluded: chain m residue 653 GLN Chi-restraints excluded: chain m residue 760 VAL Chi-restraints excluded: chain o residue 286 VAL Chi-restraints excluded: chain o residue 305 CYS Chi-restraints excluded: chain o residue 344 VAL Chi-restraints excluded: chain o residue 360 CYS Chi-restraints excluded: chain o residue 381 ILE Chi-restraints excluded: chain o residue 400 HIS Chi-restraints excluded: chain o residue 430 VAL Chi-restraints excluded: chain o residue 436 HIS Chi-restraints excluded: chain o residue 453 ILE Chi-restraints excluded: chain o residue 525 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 159 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 156 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 202 optimal weight: 2.9990 chunk 185 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 93 GLN f1009 HIS ** m 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.080741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.058706 restraints weight = 69571.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.060584 restraints weight = 35672.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.061787 restraints weight = 23301.474| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18250 Z= 0.134 Angle : 0.579 13.024 24691 Z= 0.293 Chirality : 0.041 0.154 2735 Planarity : 0.004 0.061 3192 Dihedral : 4.392 43.286 2420 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.33 % Favored : 97.63 % Rotamer: Outliers : 3.45 % Allowed : 23.93 % Favored : 72.62 % 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: 0.82 (0.18), residues: 2193 helix: 1.63 (0.16), residues: 1073 sheet: -0.81 (0.26), residues: 385 loop : -0.16 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP o 483 HIS 0.013 0.001 HIS m 769 PHE 0.019 0.001 PHE B 108 TYR 0.012 0.001 TYR o 502 ARG 0.013 0.000 ARG B 84 Details of bonding type rmsd hydrogen bonds : bond 0.04191 ( 978) hydrogen bonds : angle 4.31122 ( 2877) covalent geometry : bond 0.00289 (18250) covalent geometry : angle 0.57922 (24691) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 196 time to evaluate : 1.963 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: B 25 MET cc_start: 0.6041 (mmt) cc_final: 0.3649 (tpt) REVERT: B 96 ARG cc_start: 0.8338 (ttp80) cc_final: 0.7987 (ttp80) REVERT: B 107 LYS cc_start: 0.9378 (tmmt) cc_final: 0.8957 (tptt) REVERT: C 123 GLN cc_start: 0.9031 (tp-100) cc_final: 0.8769 (tp-100) REVERT: f 605 GLN cc_start: 0.8190 (tm-30) cc_final: 0.7773 (tm-30) REVERT: f 610 GLN cc_start: 0.8493 (tp40) cc_final: 0.8054 (tp40) REVERT: f 986 MET cc_start: 0.8500 (tpp) cc_final: 0.7954 (tmm) REVERT: f 1026 MET cc_start: 0.8178 (mmm) cc_final: 0.7747 (tpp) REVERT: j 126 GLU cc_start: 0.9033 (pp20) cc_final: 0.8812 (pp20) REVERT: j 289 HIS cc_start: 0.7948 (OUTLIER) cc_final: 0.7097 (t70) REVERT: m 622 LYS cc_start: 0.9457 (OUTLIER) cc_final: 0.9208 (ttmt) REVERT: o 426 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8091 (tt0) REVERT: o 503 ASP cc_start: 0.8457 (m-30) cc_final: 0.8113 (m-30) REVERT: o 567 GLN cc_start: 0.8597 (pm20) cc_final: 0.8302 (pm20) outliers start: 67 outliers final: 40 residues processed: 252 average time/residue: 0.3129 time to fit residues: 117.4778 Evaluate side-chains 221 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 178 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain f residue 713 VAL Chi-restraints excluded: chain f residue 746 LEU Chi-restraints excluded: chain f residue 755 TRP Chi-restraints excluded: chain f residue 823 VAL Chi-restraints excluded: chain f residue 845 GLU Chi-restraints excluded: chain f residue 888 LEU Chi-restraints excluded: chain f residue 993 VAL Chi-restraints excluded: chain h residue 344 VAL Chi-restraints excluded: chain h residue 381 ILE Chi-restraints excluded: chain h residue 406 VAL Chi-restraints excluded: chain h residue 411 MET Chi-restraints excluded: chain h residue 550 VAL Chi-restraints excluded: chain j residue 102 THR Chi-restraints excluded: chain j residue 239 VAL Chi-restraints excluded: chain j residue 240 LEU Chi-restraints excluded: chain j residue 245 ASP Chi-restraints excluded: chain j residue 258 LEU Chi-restraints excluded: chain j residue 274 VAL Chi-restraints excluded: chain j residue 289 HIS Chi-restraints excluded: chain j residue 349 VAL Chi-restraints excluded: chain m residue 339 PHE Chi-restraints excluded: chain m residue 352 LYS Chi-restraints excluded: chain m residue 472 GLN Chi-restraints excluded: chain m residue 482 ARG Chi-restraints excluded: chain m residue 576 LYS Chi-restraints excluded: chain m residue 577 ASN Chi-restraints excluded: chain m residue 622 LYS Chi-restraints excluded: chain m residue 641 LEU Chi-restraints excluded: chain m residue 653 GLN Chi-restraints excluded: chain m residue 760 VAL Chi-restraints excluded: chain o residue 311 SER Chi-restraints excluded: chain o residue 381 ILE Chi-restraints excluded: chain o residue 415 VAL Chi-restraints excluded: chain o residue 426 GLU Chi-restraints excluded: chain o residue 436 HIS Chi-restraints excluded: chain o residue 453 ILE Chi-restraints excluded: chain o residue 561 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 4 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 191 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 206 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.079996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.057977 restraints weight = 69924.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.059830 restraints weight = 36025.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.061004 restraints weight = 23660.218| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18250 Z= 0.155 Angle : 0.586 14.034 24691 Z= 0.294 Chirality : 0.041 0.202 2735 Planarity : 0.003 0.041 3192 Dihedral : 4.254 41.252 2418 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.33 % Favored : 97.63 % Rotamer: Outliers : 3.65 % Allowed : 24.03 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.18), residues: 2193 helix: 1.87 (0.16), residues: 1072 sheet: -0.86 (0.26), residues: 385 loop : -0.07 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP o 483 HIS 0.013 0.001 HIS m 769 PHE 0.023 0.001 PHE m 843 TYR 0.013 0.001 TYR o 502 ARG 0.006 0.000 ARG B 84 Details of bonding type rmsd hydrogen bonds : bond 0.04019 ( 978) hydrogen bonds : angle 4.22696 ( 2877) covalent geometry : bond 0.00336 (18250) covalent geometry : angle 0.58641 (24691) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 185 time to evaluate : 2.137 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: B 107 LYS cc_start: 0.9389 (tmmt) cc_final: 0.8981 (tptt) REVERT: B 123 GLN cc_start: 0.9065 (tm-30) cc_final: 0.8524 (mt0) REVERT: C 123 GLN cc_start: 0.9013 (tp-100) cc_final: 0.8760 (tp-100) REVERT: f 605 GLN cc_start: 0.8298 (tm-30) cc_final: 0.7976 (tm-30) REVERT: f 610 GLN cc_start: 0.8486 (tp40) cc_final: 0.7952 (tp40) REVERT: f 987 PHE cc_start: 0.5647 (OUTLIER) cc_final: 0.3923 (p90) REVERT: f 1026 MET cc_start: 0.8182 (mmm) cc_final: 0.7521 (tpp) REVERT: j 277 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8141 (mp0) REVERT: j 289 HIS cc_start: 0.7958 (OUTLIER) cc_final: 0.7103 (t70) REVERT: m 579 ASN cc_start: 0.9055 (m110) cc_final: 0.8698 (t0) REVERT: m 622 LYS cc_start: 0.9451 (OUTLIER) cc_final: 0.9201 (ttmt) REVERT: m 691 MET cc_start: 0.9134 (tpp) cc_final: 0.8928 (tpp) REVERT: o 244 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.7553 (tm-30) REVERT: o 445 MET cc_start: 0.8937 (tpp) cc_final: 0.8721 (tpp) REVERT: o 503 ASP cc_start: 0.8366 (m-30) cc_final: 0.7944 (m-30) outliers start: 71 outliers final: 48 residues processed: 243 average time/residue: 0.3075 time to fit residues: 111.9823 Evaluate side-chains 222 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 169 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain f residue 608 LEU Chi-restraints excluded: chain f residue 713 VAL Chi-restraints excluded: chain f residue 746 LEU Chi-restraints excluded: chain f residue 755 TRP Chi-restraints excluded: chain f residue 845 GLU Chi-restraints excluded: chain f residue 888 LEU Chi-restraints excluded: chain f residue 987 PHE Chi-restraints excluded: chain f residue 993 VAL Chi-restraints excluded: chain f residue 1040 VAL Chi-restraints excluded: chain h residue 344 VAL Chi-restraints excluded: chain h residue 381 ILE Chi-restraints excluded: chain h residue 406 VAL Chi-restraints excluded: chain h residue 411 MET Chi-restraints excluded: chain h residue 456 ILE Chi-restraints excluded: chain h residue 550 VAL Chi-restraints excluded: chain j residue 102 THR Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain j residue 144 THR Chi-restraints excluded: chain j residue 239 VAL Chi-restraints excluded: chain j residue 240 LEU Chi-restraints excluded: chain j residue 258 LEU Chi-restraints excluded: chain j residue 274 VAL Chi-restraints excluded: chain j residue 277 GLU Chi-restraints excluded: chain j residue 289 HIS Chi-restraints excluded: chain j residue 349 VAL Chi-restraints excluded: chain m residue 339 PHE Chi-restraints excluded: chain m residue 369 ASN Chi-restraints excluded: chain m residue 484 LEU Chi-restraints excluded: chain m residue 557 ILE Chi-restraints excluded: chain m residue 577 ASN Chi-restraints excluded: chain m residue 622 LYS Chi-restraints excluded: chain m residue 641 LEU Chi-restraints excluded: chain m residue 653 GLN Chi-restraints excluded: chain m residue 760 VAL Chi-restraints excluded: chain o residue 244 GLN Chi-restraints excluded: chain o residue 286 VAL Chi-restraints excluded: chain o residue 311 SER Chi-restraints excluded: chain o residue 344 VAL Chi-restraints excluded: chain o residue 381 ILE Chi-restraints excluded: chain o residue 415 VAL Chi-restraints excluded: chain o residue 436 HIS Chi-restraints excluded: chain o residue 453 ILE Chi-restraints excluded: chain o residue 465 VAL Chi-restraints excluded: chain o residue 561 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 85 optimal weight: 4.9990 chunk 102 optimal weight: 0.0470 chunk 208 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 126 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 205 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 overall best weight: 2.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 626 GLN f 895 ASN ** h 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.080369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.058301 restraints weight = 71232.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.060110 restraints weight = 36786.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.061247 restraints weight = 24301.714| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18250 Z= 0.174 Angle : 0.605 12.782 24691 Z= 0.303 Chirality : 0.041 0.171 2735 Planarity : 0.003 0.040 3192 Dihedral : 4.129 30.638 2414 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.55 % Favored : 97.40 % Rotamer: Outliers : 3.86 % Allowed : 24.76 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.18), residues: 2193 helix: 2.00 (0.16), residues: 1066 sheet: -0.91 (0.26), residues: 379 loop : 0.08 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP o 483 HIS 0.010 0.001 HIS m 769 PHE 0.022 0.001 PHE m 843 TYR 0.013 0.001 TYR o 502 ARG 0.005 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 978) hydrogen bonds : angle 4.20930 ( 2877) covalent geometry : bond 0.00379 (18250) covalent geometry : angle 0.60494 (24691) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 175 time to evaluate : 2.027 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: B 96 ARG cc_start: 0.8282 (ttp80) cc_final: 0.7930 (ttp80) REVERT: B 107 LYS cc_start: 0.9405 (tmmt) cc_final: 0.8992 (tptt) REVERT: C 107 LYS cc_start: 0.9430 (OUTLIER) cc_final: 0.8874 (pttm) REVERT: C 123 GLN cc_start: 0.9034 (tp-100) cc_final: 0.8782 (tp-100) REVERT: f 605 GLN cc_start: 0.8347 (tm-30) cc_final: 0.8003 (tm-30) REVERT: f 610 GLN cc_start: 0.8462 (tp40) cc_final: 0.7792 (tp40) REVERT: f 624 LYS cc_start: 0.9551 (mmmm) cc_final: 0.8941 (mmmm) REVERT: f 987 PHE cc_start: 0.5763 (OUTLIER) cc_final: 0.4126 (p90) REVERT: f 1026 MET cc_start: 0.8479 (mmm) cc_final: 0.8131 (mmm) REVERT: j 163 MET cc_start: 0.6993 (pmm) cc_final: 0.6701 (pmm) REVERT: j 277 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8164 (mp0) REVERT: j 289 HIS cc_start: 0.7961 (OUTLIER) cc_final: 0.7106 (t70) REVERT: m 579 ASN cc_start: 0.9063 (m110) cc_final: 0.8712 (t0) REVERT: m 602 ARG cc_start: 0.8505 (mmm-85) cc_final: 0.8163 (mmm-85) REVERT: m 622 LYS cc_start: 0.9457 (OUTLIER) cc_final: 0.9253 (ttmt) REVERT: o 244 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.7587 (tm-30) REVERT: o 503 ASP cc_start: 0.8389 (m-30) cc_final: 0.7930 (m-30) REVERT: o 548 ASN cc_start: 0.9101 (t0) cc_final: 0.8540 (t0) outliers start: 75 outliers final: 50 residues processed: 234 average time/residue: 0.3174 time to fit residues: 109.9869 Evaluate side-chains 219 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 163 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 128 HIS Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain f residue 608 LEU Chi-restraints excluded: chain f residue 713 VAL Chi-restraints excluded: chain f residue 746 LEU Chi-restraints excluded: chain f residue 755 TRP Chi-restraints excluded: chain f residue 815 LEU Chi-restraints excluded: chain f residue 823 VAL Chi-restraints excluded: chain f residue 845 GLU Chi-restraints excluded: chain f residue 888 LEU Chi-restraints excluded: chain f residue 987 PHE Chi-restraints excluded: chain f residue 993 VAL Chi-restraints excluded: chain f residue 1040 VAL Chi-restraints excluded: chain h residue 342 THR Chi-restraints excluded: chain h residue 344 VAL Chi-restraints excluded: chain h residue 381 ILE Chi-restraints excluded: chain h residue 406 VAL Chi-restraints excluded: chain h residue 411 MET Chi-restraints excluded: chain h residue 456 ILE Chi-restraints excluded: chain h residue 550 VAL Chi-restraints excluded: chain j residue 239 VAL Chi-restraints excluded: chain j residue 240 LEU Chi-restraints excluded: chain j residue 258 LEU Chi-restraints excluded: chain j residue 274 VAL Chi-restraints excluded: chain j residue 277 GLU Chi-restraints excluded: chain j residue 289 HIS Chi-restraints excluded: chain m residue 339 PHE Chi-restraints excluded: chain m residue 352 LYS Chi-restraints excluded: chain m residue 484 LEU Chi-restraints excluded: chain m residue 557 ILE Chi-restraints excluded: chain m residue 577 ASN Chi-restraints excluded: chain m residue 622 LYS Chi-restraints excluded: chain m residue 641 LEU Chi-restraints excluded: chain m residue 653 GLN Chi-restraints excluded: chain m residue 760 VAL Chi-restraints excluded: chain o residue 244 GLN Chi-restraints excluded: chain o residue 286 VAL Chi-restraints excluded: chain o residue 305 CYS Chi-restraints excluded: chain o residue 311 SER Chi-restraints excluded: chain o residue 344 VAL Chi-restraints excluded: chain o residue 360 CYS Chi-restraints excluded: chain o residue 381 ILE Chi-restraints excluded: chain o residue 415 VAL Chi-restraints excluded: chain o residue 436 HIS Chi-restraints excluded: chain o residue 453 ILE Chi-restraints excluded: chain o residue 465 VAL Chi-restraints excluded: chain o residue 561 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 46 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 120 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 206 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 31 optimal weight: 20.0000 chunk 119 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 221 HIS ** m 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 657 GLN ** m 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 242 ASN ** o 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.079129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.057155 restraints weight = 71309.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.058905 restraints weight = 37128.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.060022 restraints weight = 24669.129| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 18250 Z= 0.230 Angle : 0.646 13.592 24691 Z= 0.327 Chirality : 0.042 0.180 2735 Planarity : 0.004 0.038 3192 Dihedral : 4.306 36.623 2414 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.83 % Favored : 97.13 % Rotamer: Outliers : 4.63 % Allowed : 24.76 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.19), residues: 2193 helix: 1.92 (0.16), residues: 1067 sheet: -1.11 (0.25), residues: 393 loop : 0.15 (0.24), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP o 483 HIS 0.008 0.001 HIS m 769 PHE 0.024 0.002 PHE m 843 TYR 0.014 0.001 TYR o 502 ARG 0.007 0.001 ARG f1003 Details of bonding type rmsd hydrogen bonds : bond 0.04112 ( 978) hydrogen bonds : angle 4.34561 ( 2877) covalent geometry : bond 0.00501 (18250) covalent geometry : angle 0.64572 (24691) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 177 time to evaluate : 2.017 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: B 107 LYS cc_start: 0.9412 (tmmt) cc_final: 0.9001 (tptt) REVERT: B 123 GLN cc_start: 0.9156 (tm-30) cc_final: 0.8603 (mt0) REVERT: C 123 GLN cc_start: 0.9027 (tp-100) cc_final: 0.8787 (tp-100) REVERT: f 605 GLN cc_start: 0.8419 (tm-30) cc_final: 0.7944 (tm-30) REVERT: f 610 GLN cc_start: 0.8485 (tp40) cc_final: 0.7748 (tp40) REVERT: f 624 LYS cc_start: 0.9559 (mmmm) cc_final: 0.8935 (mmmm) REVERT: f 987 PHE cc_start: 0.5848 (OUTLIER) cc_final: 0.4167 (p90) REVERT: f 1026 MET cc_start: 0.8561 (mmm) cc_final: 0.8063 (mmm) REVERT: j 277 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8163 (mp0) REVERT: j 289 HIS cc_start: 0.7966 (OUTLIER) cc_final: 0.7153 (t70) REVERT: m 413 MET cc_start: 0.9245 (ppp) cc_final: 0.8998 (ppp) REVERT: m 466 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.9053 (ttp) REVERT: m 579 ASN cc_start: 0.8992 (m110) cc_final: 0.8703 (t0) REVERT: m 602 ARG cc_start: 0.8523 (mmm-85) cc_final: 0.8150 (mmm-85) REVERT: o 244 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.7648 (tm-30) REVERT: o 265 TYR cc_start: 0.7268 (OUTLIER) cc_final: 0.6775 (m-80) REVERT: o 503 ASP cc_start: 0.8398 (m-30) cc_final: 0.8059 (m-30) REVERT: o 548 ASN cc_start: 0.9188 (t0) cc_final: 0.8853 (t0) outliers start: 90 outliers final: 60 residues processed: 249 average time/residue: 0.3113 time to fit residues: 115.3353 Evaluate side-chains 235 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 169 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 128 HIS Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain f residue 608 LEU Chi-restraints excluded: chain f residue 713 VAL Chi-restraints excluded: chain f residue 746 LEU Chi-restraints excluded: chain f residue 755 TRP Chi-restraints excluded: chain f residue 815 LEU Chi-restraints excluded: chain f residue 823 VAL Chi-restraints excluded: chain f residue 845 GLU Chi-restraints excluded: chain f residue 888 LEU Chi-restraints excluded: chain f residue 987 PHE Chi-restraints excluded: chain f residue 993 VAL Chi-restraints excluded: chain f residue 1040 VAL Chi-restraints excluded: chain h residue 342 THR Chi-restraints excluded: chain h residue 344 VAL Chi-restraints excluded: chain h residue 381 ILE Chi-restraints excluded: chain h residue 406 VAL Chi-restraints excluded: chain h residue 411 MET Chi-restraints excluded: chain h residue 456 ILE Chi-restraints excluded: chain h residue 495 GLU Chi-restraints excluded: chain h residue 550 VAL Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain j residue 144 THR Chi-restraints excluded: chain j residue 239 VAL Chi-restraints excluded: chain j residue 240 LEU Chi-restraints excluded: chain j residue 245 ASP Chi-restraints excluded: chain j residue 258 LEU Chi-restraints excluded: chain j residue 274 VAL Chi-restraints excluded: chain j residue 277 GLU Chi-restraints excluded: chain j residue 289 HIS Chi-restraints excluded: chain m residue 339 PHE Chi-restraints excluded: chain m residue 352 LYS Chi-restraints excluded: chain m residue 369 ASN Chi-restraints excluded: chain m residue 466 MET Chi-restraints excluded: chain m residue 484 LEU Chi-restraints excluded: chain m residue 557 ILE Chi-restraints excluded: chain m residue 577 ASN Chi-restraints excluded: chain m residue 760 VAL Chi-restraints excluded: chain o residue 244 GLN Chi-restraints excluded: chain o residue 265 TYR Chi-restraints excluded: chain o residue 286 VAL Chi-restraints excluded: chain o residue 305 CYS Chi-restraints excluded: chain o residue 311 SER Chi-restraints excluded: chain o residue 344 VAL Chi-restraints excluded: chain o residue 360 CYS Chi-restraints excluded: chain o residue 381 ILE Chi-restraints excluded: chain o residue 415 VAL Chi-restraints excluded: chain o residue 418 VAL Chi-restraints excluded: chain o residue 430 VAL Chi-restraints excluded: chain o residue 436 HIS Chi-restraints excluded: chain o residue 453 ILE Chi-restraints excluded: chain o residue 465 VAL Chi-restraints excluded: chain o residue 475 SER Chi-restraints excluded: chain o residue 561 VAL Chi-restraints excluded: chain o residue 564 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 201 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 199 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 chunk 105 optimal weight: 0.0060 chunk 188 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 895 ASN j 221 HIS ** m 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.080120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.058149 restraints weight = 69362.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.060009 restraints weight = 35413.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.061192 restraints weight = 23200.109| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18250 Z= 0.115 Angle : 0.624 14.456 24691 Z= 0.304 Chirality : 0.042 0.198 2735 Planarity : 0.003 0.039 3192 Dihedral : 4.084 30.191 2414 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.10 % Favored : 97.86 % Rotamer: Outliers : 2.93 % Allowed : 26.61 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.19), residues: 2193 helix: 2.02 (0.16), residues: 1059 sheet: -0.95 (0.25), residues: 389 loop : 0.24 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP o 483 HIS 0.007 0.001 HIS m 769 PHE 0.015 0.001 PHE m 843 TYR 0.009 0.001 TYR j 336 ARG 0.007 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03870 ( 978) hydrogen bonds : angle 4.13795 ( 2877) covalent geometry : bond 0.00248 (18250) covalent geometry : angle 0.62353 (24691) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 195 time to evaluate : 2.112 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: B 96 ARG cc_start: 0.8236 (ttp80) cc_final: 0.7951 (ttp80) REVERT: B 107 LYS cc_start: 0.9390 (tmmt) cc_final: 0.9012 (tptt) REVERT: C 93 GLN cc_start: 0.8873 (tt0) cc_final: 0.8585 (tt0) REVERT: C 107 LYS cc_start: 0.9265 (pttm) cc_final: 0.8986 (pttm) REVERT: C 128 HIS cc_start: 0.4379 (OUTLIER) cc_final: 0.4039 (p-80) REVERT: f 581 MET cc_start: 0.9454 (ttm) cc_final: 0.9230 (mtp) REVERT: f 605 GLN cc_start: 0.8432 (tm-30) cc_final: 0.8054 (tm-30) REVERT: f 610 GLN cc_start: 0.8527 (tp40) cc_final: 0.7838 (tp40) REVERT: f 624 LYS cc_start: 0.9573 (mmmm) cc_final: 0.8935 (mmmm) REVERT: f 1026 MET cc_start: 0.8409 (mmm) cc_final: 0.8019 (mmm) REVERT: h 388 MET cc_start: 0.8543 (tpp) cc_final: 0.8132 (tpp) REVERT: j 163 MET cc_start: 0.6907 (pmm) cc_final: 0.6640 (pmm) REVERT: j 277 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8191 (mp0) REVERT: j 289 HIS cc_start: 0.7813 (OUTLIER) cc_final: 0.6954 (t70) REVERT: m 579 ASN cc_start: 0.9032 (m110) cc_final: 0.8686 (t0) REVERT: m 602 ARG cc_start: 0.8445 (mmm-85) cc_final: 0.8092 (mmm-85) REVERT: o 244 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.7578 (tm-30) REVERT: o 503 ASP cc_start: 0.8331 (m-30) cc_final: 0.7925 (m-30) REVERT: o 548 ASN cc_start: 0.9028 (t0) cc_final: 0.8504 (t0) outliers start: 57 outliers final: 40 residues processed: 235 average time/residue: 0.3260 time to fit residues: 114.3343 Evaluate side-chains 221 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 128 HIS Chi-restraints excluded: chain C residue 28 ARG Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 128 HIS Chi-restraints excluded: chain f residue 713 VAL Chi-restraints excluded: chain f residue 746 LEU Chi-restraints excluded: chain f residue 755 TRP Chi-restraints excluded: chain f residue 801 ILE Chi-restraints excluded: chain f residue 815 LEU Chi-restraints excluded: chain f residue 823 VAL Chi-restraints excluded: chain f residue 845 GLU Chi-restraints excluded: chain f residue 888 LEU Chi-restraints excluded: chain f residue 993 VAL Chi-restraints excluded: chain f residue 1040 VAL Chi-restraints excluded: chain h residue 344 VAL Chi-restraints excluded: chain h residue 381 ILE Chi-restraints excluded: chain h residue 406 VAL Chi-restraints excluded: chain h residue 411 MET Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain j residue 144 THR Chi-restraints excluded: chain j residue 239 VAL Chi-restraints excluded: chain j residue 240 LEU Chi-restraints excluded: chain j residue 258 LEU Chi-restraints excluded: chain j residue 274 VAL Chi-restraints excluded: chain j residue 277 GLU Chi-restraints excluded: chain j residue 289 HIS Chi-restraints excluded: chain m residue 577 ASN Chi-restraints excluded: chain m residue 641 LEU Chi-restraints excluded: chain m residue 760 VAL Chi-restraints excluded: chain o residue 244 GLN Chi-restraints excluded: chain o residue 269 LEU Chi-restraints excluded: chain o residue 286 VAL Chi-restraints excluded: chain o residue 311 SER Chi-restraints excluded: chain o residue 415 VAL Chi-restraints excluded: chain o residue 436 HIS Chi-restraints excluded: chain o residue 465 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 218 optimal weight: 9.9990 chunk 194 optimal weight: 7.9990 chunk 188 optimal weight: 9.9990 chunk 41 optimal weight: 0.0970 chunk 126 optimal weight: 0.0370 chunk 200 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 63 optimal weight: 0.0670 chunk 98 optimal weight: 5.9990 chunk 169 optimal weight: 0.5980 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS ** m 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 487 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 = 0.3600 r_free = 0.3600 target = 0.080741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.058754 restraints weight = 69311.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.060659 restraints weight = 35182.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.061872 restraints weight = 22879.022| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 18250 Z= 0.113 Angle : 0.633 14.994 24691 Z= 0.307 Chirality : 0.042 0.312 2735 Planarity : 0.003 0.039 3192 Dihedral : 3.960 27.047 2412 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.10 % Favored : 97.86 % Rotamer: Outliers : 2.62 % Allowed : 27.12 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.19), residues: 2193 helix: 1.98 (0.16), residues: 1073 sheet: -0.85 (0.26), residues: 379 loop : 0.21 (0.24), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP m 755 HIS 0.007 0.001 HIS m 769 PHE 0.020 0.001 PHE m 843 TYR 0.010 0.001 TYR h 502 ARG 0.008 0.000 ARG B 84 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 978) hydrogen bonds : angle 4.09724 ( 2877) covalent geometry : bond 0.00249 (18250) covalent geometry : angle 0.63311 (24691) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 191 time to evaluate : 2.071 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: B 96 ARG cc_start: 0.8476 (ttp80) cc_final: 0.8086 (ttp80) REVERT: B 107 LYS cc_start: 0.9375 (tmmt) cc_final: 0.9002 (tptt) REVERT: B 108 PHE cc_start: 0.9059 (t80) cc_final: 0.8396 (t80) REVERT: B 123 GLN cc_start: 0.9120 (tm-30) cc_final: 0.8455 (mt0) REVERT: C 107 LYS cc_start: 0.9389 (pttm) cc_final: 0.8947 (ptpp) REVERT: C 128 HIS cc_start: 0.4574 (OUTLIER) cc_final: 0.4221 (p-80) REVERT: f 581 MET cc_start: 0.9456 (ttm) cc_final: 0.9223 (mtp) REVERT: f 605 GLN cc_start: 0.8424 (tm-30) cc_final: 0.8038 (tm-30) REVERT: f 610 GLN cc_start: 0.8528 (tp40) cc_final: 0.7825 (tp40) REVERT: f 624 LYS cc_start: 0.9553 (mmmm) cc_final: 0.8924 (mmmm) REVERT: j 163 MET cc_start: 0.6902 (pmm) cc_final: 0.6646 (pmm) REVERT: j 277 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8201 (mp0) REVERT: j 289 HIS cc_start: 0.7803 (OUTLIER) cc_final: 0.6957 (t70) REVERT: m 413 MET cc_start: 0.9300 (ppp) cc_final: 0.9039 (ppp) REVERT: m 579 ASN cc_start: 0.9008 (m110) cc_final: 0.8693 (t0) REVERT: m 602 ARG cc_start: 0.8425 (mmm-85) cc_final: 0.8096 (mmm-85) REVERT: o 244 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.7574 (tm-30) REVERT: o 445 MET cc_start: 0.8759 (tpp) cc_final: 0.8442 (tpp) REVERT: o 503 ASP cc_start: 0.8439 (m-30) cc_final: 0.8013 (m-30) REVERT: o 548 ASN cc_start: 0.9008 (t0) cc_final: 0.8574 (t0) outliers start: 51 outliers final: 34 residues processed: 228 average time/residue: 0.3180 time to fit residues: 107.9664 Evaluate side-chains 214 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 128 HIS Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 128 HIS Chi-restraints excluded: chain f residue 682 LEU Chi-restraints excluded: chain f residue 713 VAL Chi-restraints excluded: chain f residue 746 LEU Chi-restraints excluded: chain f residue 755 TRP Chi-restraints excluded: chain f residue 801 ILE Chi-restraints excluded: chain f residue 815 LEU Chi-restraints excluded: chain f residue 823 VAL Chi-restraints excluded: chain f residue 845 GLU Chi-restraints excluded: chain f residue 993 VAL Chi-restraints excluded: chain f residue 1040 VAL Chi-restraints excluded: chain h residue 381 ILE Chi-restraints excluded: chain h residue 406 VAL Chi-restraints excluded: chain h residue 411 MET Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain j residue 144 THR Chi-restraints excluded: chain j residue 239 VAL Chi-restraints excluded: chain j residue 258 LEU Chi-restraints excluded: chain j residue 274 VAL Chi-restraints excluded: chain j residue 277 GLU Chi-restraints excluded: chain j residue 289 HIS Chi-restraints excluded: chain m residue 577 ASN Chi-restraints excluded: chain m residue 641 LEU Chi-restraints excluded: chain m residue 760 VAL Chi-restraints excluded: chain o residue 244 GLN Chi-restraints excluded: chain o residue 269 LEU Chi-restraints excluded: chain o residue 286 VAL Chi-restraints excluded: chain o residue 311 SER Chi-restraints excluded: chain o residue 436 HIS Chi-restraints excluded: chain o residue 465 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 15 optimal weight: 5.9990 chunk 135 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 144 optimal weight: 7.9990 chunk 193 optimal weight: 3.9990 chunk 188 optimal weight: 8.9990 chunk 132 optimal weight: 0.1980 chunk 63 optimal weight: 8.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 276 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 = 0.3561 r_free = 0.3561 target = 0.078875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.057005 restraints weight = 70245.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.058818 restraints weight = 36078.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.059986 restraints weight = 23709.119| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18250 Z= 0.198 Angle : 0.682 14.503 24691 Z= 0.337 Chirality : 0.043 0.280 2735 Planarity : 0.004 0.039 3192 Dihedral : 4.092 24.301 2412 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.83 % Favored : 97.13 % Rotamer: Outliers : 2.93 % Allowed : 27.02 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.19), residues: 2193 helix: 1.95 (0.16), residues: 1067 sheet: -1.04 (0.25), residues: 391 loop : 0.27 (0.25), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP m 755 HIS 0.006 0.001 HIS m 473 PHE 0.045 0.002 PHE C 111 TYR 0.014 0.001 TYR o 502 ARG 0.016 0.000 ARG B 84 Details of bonding type rmsd hydrogen bonds : bond 0.03899 ( 978) hydrogen bonds : angle 4.24950 ( 2877) covalent geometry : bond 0.00439 (18250) covalent geometry : angle 0.68208 (24691) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 179 time to evaluate : 2.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 ARG cc_start: 0.8472 (ttp80) cc_final: 0.8079 (ttp80) REVERT: B 107 LYS cc_start: 0.9408 (tmmt) cc_final: 0.8983 (tptt) REVERT: C 107 LYS cc_start: 0.9335 (pttm) cc_final: 0.9023 (ptpp) REVERT: C 128 HIS cc_start: 0.4561 (OUTLIER) cc_final: 0.4224 (p-80) REVERT: f 605 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8121 (tm-30) REVERT: f 610 GLN cc_start: 0.8566 (tp40) cc_final: 0.7852 (tp40) REVERT: f 624 LYS cc_start: 0.9575 (mmmm) cc_final: 0.8949 (mmmm) REVERT: f 663 LYS cc_start: 0.8982 (tppt) cc_final: 0.8711 (tppt) REVERT: h 388 MET cc_start: 0.8570 (tpp) cc_final: 0.8233 (tpp) REVERT: j 170 MET cc_start: 0.8173 (ppp) cc_final: 0.7679 (ppp) REVERT: j 277 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8224 (mp0) REVERT: j 289 HIS cc_start: 0.7943 (OUTLIER) cc_final: 0.7129 (t70) REVERT: m 413 MET cc_start: 0.9226 (ppp) cc_final: 0.8989 (ppp) REVERT: m 579 ASN cc_start: 0.9061 (m110) cc_final: 0.8764 (t0) REVERT: m 602 ARG cc_start: 0.8527 (mmm-85) cc_final: 0.8172 (mmm-85) REVERT: m 846 LYS cc_start: 0.9143 (mmtm) cc_final: 0.8932 (mmtm) REVERT: o 244 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.7620 (tm-30) REVERT: o 445 MET cc_start: 0.9041 (tpp) cc_final: 0.8480 (tpp) REVERT: o 503 ASP cc_start: 0.8432 (m-30) cc_final: 0.8007 (m-30) REVERT: o 548 ASN cc_start: 0.9186 (t0) cc_final: 0.8773 (t0) outliers start: 57 outliers final: 42 residues processed: 224 average time/residue: 0.3232 time to fit residues: 108.0898 Evaluate side-chains 219 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 173 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 128 HIS Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 128 HIS Chi-restraints excluded: chain f residue 713 VAL Chi-restraints excluded: chain f residue 746 LEU Chi-restraints excluded: chain f residue 755 TRP Chi-restraints excluded: chain f residue 801 ILE Chi-restraints excluded: chain f residue 815 LEU Chi-restraints excluded: chain f residue 823 VAL Chi-restraints excluded: chain f residue 845 GLU Chi-restraints excluded: chain f residue 857 ILE Chi-restraints excluded: chain f residue 993 VAL Chi-restraints excluded: chain f residue 1040 VAL Chi-restraints excluded: chain h residue 344 VAL Chi-restraints excluded: chain h residue 381 ILE Chi-restraints excluded: chain h residue 406 VAL Chi-restraints excluded: chain h residue 411 MET Chi-restraints excluded: chain h residue 573 VAL Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain j residue 144 THR Chi-restraints excluded: chain j residue 239 VAL Chi-restraints excluded: chain j residue 240 LEU Chi-restraints excluded: chain j residue 245 ASP Chi-restraints excluded: chain j residue 258 LEU Chi-restraints excluded: chain j residue 274 VAL Chi-restraints excluded: chain j residue 277 GLU Chi-restraints excluded: chain j residue 289 HIS Chi-restraints excluded: chain m residue 339 PHE Chi-restraints excluded: chain m residue 557 ILE Chi-restraints excluded: chain m residue 577 ASN Chi-restraints excluded: chain m residue 641 LEU Chi-restraints excluded: chain m residue 760 VAL Chi-restraints excluded: chain o residue 244 GLN Chi-restraints excluded: chain o residue 269 LEU Chi-restraints excluded: chain o residue 286 VAL Chi-restraints excluded: chain o residue 311 SER Chi-restraints excluded: chain o residue 381 ILE Chi-restraints excluded: chain o residue 436 HIS Chi-restraints excluded: chain o residue 465 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 6 optimal weight: 0.9990 chunk 172 optimal weight: 0.7980 chunk 189 optimal weight: 6.9990 chunk 163 optimal weight: 0.9990 chunk 117 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 154 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN ** m 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.080460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.058539 restraints weight = 69393.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.060410 restraints weight = 35294.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.061623 restraints weight = 23054.983| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18250 Z= 0.119 Angle : 0.666 15.605 24691 Z= 0.323 Chirality : 0.042 0.301 2735 Planarity : 0.003 0.040 3192 Dihedral : 3.961 21.696 2412 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.26 % Allowed : 27.69 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.19), residues: 2193 helix: 1.93 (0.16), residues: 1076 sheet: -0.95 (0.26), residues: 391 loop : 0.27 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP m 755 HIS 0.007 0.001 HIS m 769 PHE 0.034 0.001 PHE B 108 TYR 0.010 0.001 TYR o 431 ARG 0.009 0.000 ARG B 84 Details of bonding type rmsd hydrogen bonds : bond 0.03780 ( 978) hydrogen bonds : angle 4.12725 ( 2877) covalent geometry : bond 0.00265 (18250) covalent geometry : angle 0.66566 (24691) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 185 time to evaluate : 2.015 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: B 96 ARG cc_start: 0.8418 (ttp80) cc_final: 0.8030 (ttp80) REVERT: B 107 LYS cc_start: 0.9398 (tmmt) cc_final: 0.8984 (tptt) REVERT: C 128 HIS cc_start: 0.4562 (OUTLIER) cc_final: 0.4274 (p-80) REVERT: f 581 MET cc_start: 0.9470 (ttm) cc_final: 0.9252 (mtp) REVERT: f 605 GLN cc_start: 0.8453 (tm-30) cc_final: 0.8085 (tm-30) REVERT: f 610 GLN cc_start: 0.8529 (tp40) cc_final: 0.7821 (tp40) REVERT: f 624 LYS cc_start: 0.9557 (mmmm) cc_final: 0.8930 (mmmm) REVERT: h 388 MET cc_start: 0.8472 (tpp) cc_final: 0.8133 (tpp) REVERT: j 163 MET cc_start: 0.6819 (pmm) cc_final: 0.6566 (pmm) REVERT: j 277 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8213 (mp0) REVERT: j 289 HIS cc_start: 0.7748 (OUTLIER) cc_final: 0.6901 (t70) REVERT: m 413 MET cc_start: 0.9260 (ppp) cc_final: 0.8978 (ppp) REVERT: m 579 ASN cc_start: 0.9020 (m110) cc_final: 0.8711 (t0) REVERT: m 602 ARG cc_start: 0.8441 (mmm-85) cc_final: 0.8106 (mmm-85) REVERT: m 635 MET cc_start: 0.9506 (mmm) cc_final: 0.9196 (mmp) REVERT: m 846 LYS cc_start: 0.9135 (mmtm) cc_final: 0.8918 (mmtm) REVERT: o 244 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.7561 (tm-30) REVERT: o 445 MET cc_start: 0.8752 (tpp) cc_final: 0.8517 (tpp) REVERT: o 503 ASP cc_start: 0.8378 (m-30) cc_final: 0.7919 (m-30) REVERT: o 548 ASN cc_start: 0.9066 (t0) cc_final: 0.8252 (t0) outliers start: 44 outliers final: 34 residues processed: 217 average time/residue: 0.3264 time to fit residues: 106.1492 Evaluate side-chains 216 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 128 HIS Chi-restraints excluded: chain C residue 45 HIS Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 128 HIS Chi-restraints excluded: chain f residue 713 VAL Chi-restraints excluded: chain f residue 746 LEU Chi-restraints excluded: chain f residue 755 TRP Chi-restraints excluded: chain f residue 801 ILE Chi-restraints excluded: chain f residue 823 VAL Chi-restraints excluded: chain f residue 845 GLU Chi-restraints excluded: chain f residue 993 VAL Chi-restraints excluded: chain f residue 1040 VAL Chi-restraints excluded: chain h residue 344 VAL Chi-restraints excluded: chain h residue 381 ILE Chi-restraints excluded: chain h residue 406 VAL Chi-restraints excluded: chain h residue 411 MET Chi-restraints excluded: chain h residue 573 VAL Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain j residue 144 THR Chi-restraints excluded: chain j residue 239 VAL Chi-restraints excluded: chain j residue 240 LEU Chi-restraints excluded: chain j residue 258 LEU Chi-restraints excluded: chain j residue 274 VAL Chi-restraints excluded: chain j residue 277 GLU Chi-restraints excluded: chain j residue 289 HIS Chi-restraints excluded: chain m residue 577 ASN Chi-restraints excluded: chain m residue 641 LEU Chi-restraints excluded: chain m residue 760 VAL Chi-restraints excluded: chain o residue 244 GLN Chi-restraints excluded: chain o residue 269 LEU Chi-restraints excluded: chain o residue 286 VAL Chi-restraints excluded: chain o residue 311 SER Chi-restraints excluded: chain o residue 436 HIS Chi-restraints excluded: chain o residue 465 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 35 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 163 optimal weight: 8.9990 chunk 167 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 276 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 = 0.3556 r_free = 0.3556 target = 0.078664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.056736 restraints weight = 70304.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.058554 restraints weight = 36267.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.059704 restraints weight = 23794.394| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18250 Z= 0.204 Angle : 0.691 15.172 24691 Z= 0.342 Chirality : 0.043 0.285 2735 Planarity : 0.004 0.042 3192 Dihedral : 4.104 23.666 2412 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.92 % Favored : 97.04 % Rotamer: Outliers : 2.32 % Allowed : 27.95 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.19), residues: 2193 helix: 1.90 (0.16), residues: 1074 sheet: -1.08 (0.25), residues: 391 loop : 0.22 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP m 755 HIS 0.007 0.001 HIS m 473 PHE 0.025 0.002 PHE m 582 TYR 0.015 0.001 TYR h 502 ARG 0.007 0.000 ARG f1003 Details of bonding type rmsd hydrogen bonds : bond 0.03928 ( 978) hydrogen bonds : angle 4.28866 ( 2877) covalent geometry : bond 0.00449 (18250) covalent geometry : angle 0.69126 (24691) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5361.59 seconds wall clock time: 95 minutes 20.36 seconds (5720.36 seconds total)