Starting phenix.real_space_refine on Thu Sep 18 15:36:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pr3_17833/09_2025/8pr3_17833.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pr3_17833/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8pr3_17833/09_2025/8pr3_17833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pr3_17833/09_2025/8pr3_17833.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pr3_17833/09_2025/8pr3_17833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pr3_17833/09_2025/8pr3_17833.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.32, per 1000 atoms: 0.19 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: 1.20 Conformation dependent library (CDL) restraints added in 716.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.45 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: 2.71 Time building geometry restraints manager: 1.69 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.310 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.470 ------------------------------------------------------------------------------- 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 : 6.08 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.015 0.001 ARG f1020 TYR 0.022 0.002 TYR h 301 PHE 0.033 0.002 PHE m 843 TRP 0.014 0.002 TRP h 552 HIS 0.011 0.001 HIS o 400 Details of bonding type rmsd covalent geometry : bond 0.00590 (18250) covalent geometry : angle 1.07887 (24691) hydrogen bonds : bond 0.15997 ( 978) hydrogen bonds : angle 6.54056 ( 2877) *********************** 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 : 0.547 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: 0.1443 time to fit residues: 47.1476 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 : 0.693 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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** ** 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.082113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.060018 restraints weight = 69034.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.061955 restraints weight = 34975.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.063176 restraints weight = 22730.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.063949 restraints weight = 17348.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.064391 restraints weight = 14674.813| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18250 Z= 0.116 Angle : 0.598 11.476 24691 Z= 0.303 Chirality : 0.041 0.146 2735 Planarity : 0.004 0.049 3192 Dihedral : 4.746 47.388 2426 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.92 % Favored : 98.04 % Rotamer: Outliers : 1.96 % Allowed : 24.19 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.18), residues: 2193 helix: 1.03 (0.16), residues: 1066 sheet: -0.71 (0.27), residues: 363 loop : -0.50 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG j 103 TYR 0.011 0.001 TYR o 502 PHE 0.015 0.001 PHE h 476 TRP 0.013 0.001 TRP j 143 HIS 0.003 0.001 HIS j 250 Details of bonding type rmsd covalent geometry : bond 0.00238 (18250) covalent geometry : angle 0.59764 (24691) hydrogen bonds : bond 0.04469 ( 978) hydrogen bonds : angle 4.52786 ( 2877) *********************** 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 245 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 207 time to evaluate : 0.702 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 25 MET cc_start: 0.6380 (mmt) cc_final: 0.3826 (tpt) REVERT: B 107 LYS cc_start: 0.9355 (tmmt) cc_final: 0.9007 (tptt) REVERT: C 123 GLN cc_start: 0.9030 (tp-100) cc_final: 0.8768 (tp-100) REVERT: f 605 GLN cc_start: 0.8102 (tm-30) cc_final: 0.7776 (tm-30) REVERT: f 610 GLN cc_start: 0.8327 (tp40) cc_final: 0.8057 (tp40) REVERT: m 413 MET cc_start: 0.9174 (ppp) cc_final: 0.8862 (ppp) REVERT: o 310 MET cc_start: 0.8549 (ptp) cc_final: 0.8336 (mtm) REVERT: o 400 HIS cc_start: 0.7054 (OUTLIER) cc_final: 0.6465 (t70) REVERT: o 567 GLN cc_start: 0.8447 (pm20) cc_final: 0.8210 (pm20) outliers start: 38 outliers final: 23 residues processed: 238 average time/residue: 0.1408 time to fit residues: 49.6302 Evaluate side-chains 198 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 106 GLU Chi-restraints excluded: chain f residue 713 VAL Chi-restraints excluded: chain f residue 746 LEU Chi-restraints excluded: chain f residue 770 GLN Chi-restraints excluded: chain f residue 845 GLU 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 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 o residue 305 CYS Chi-restraints excluded: chain o residue 381 ILE Chi-restraints excluded: chain o residue 400 HIS Chi-restraints excluded: chain o residue 436 HIS 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 149 optimal weight: 9.9990 chunk 136 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 12 optimal weight: 0.3980 chunk 181 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- 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 C 87 ASN ** f 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f1009 HIS ** h 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 576 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** ** m 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 469 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.079824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.058392 restraints weight = 71078.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.060134 restraints weight = 37005.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.061246 restraints weight = 24503.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.061950 restraints weight = 18893.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.062246 restraints weight = 16122.259| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 18250 Z= 0.236 Angle : 0.642 12.175 24691 Z= 0.331 Chirality : 0.042 0.146 2735 Planarity : 0.004 0.047 3192 Dihedral : 4.536 42.376 2419 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.83 % Favored : 97.13 % Rotamer: Outliers : 4.01 % Allowed : 23.93 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.18), residues: 2193 helix: 1.59 (0.16), residues: 1067 sheet: -0.88 (0.26), residues: 391 loop : -0.18 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 84 TYR 0.018 0.002 TYR o 502 PHE 0.013 0.002 PHE h 588 TRP 0.018 0.001 TRP m 755 HIS 0.013 0.001 HIS m 769 Details of bonding type rmsd covalent geometry : bond 0.00508 (18250) covalent geometry : angle 0.64232 (24691) hydrogen bonds : bond 0.04412 ( 978) hydrogen bonds : angle 4.46386 ( 2877) *********************** 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 253 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 175 time to evaluate : 0.632 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: 0.8337 (ttp80) cc_final: 0.8002 (ttp80) REVERT: B 98 LYS cc_start: 0.9364 (tppt) cc_final: 0.9131 (tppt) REVERT: B 107 LYS cc_start: 0.9399 (tmmt) cc_final: 0.8995 (tptt) REVERT: C 93 GLN cc_start: 0.8672 (tt0) cc_final: 0.8355 (tt0) REVERT: C 123 GLN cc_start: 0.9017 (tp-100) cc_final: 0.8761 (tp-100) REVERT: f 605 GLN cc_start: 0.8256 (tm-30) cc_final: 0.7852 (tm-30) REVERT: f 610 GLN cc_start: 0.8476 (tp40) cc_final: 0.8016 (tp40) REVERT: f 987 PHE cc_start: 0.5776 (OUTLIER) cc_final: 0.3945 (p90) REVERT: j 289 HIS cc_start: 0.7941 (OUTLIER) cc_final: 0.7073 (t70) REVERT: m 622 LYS cc_start: 0.9457 (OUTLIER) cc_final: 0.9219 (ttmt) REVERT: m 691 MET cc_start: 0.9061 (tpp) cc_final: 0.8831 (tpp) REVERT: o 310 MET cc_start: 0.8635 (ptp) cc_final: 0.8353 (mtm) outliers start: 78 outliers final: 49 residues processed: 236 average time/residue: 0.1473 time to fit residues: 51.5124 Evaluate side-chains 208 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 156 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 80 LEU 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 106 GLU 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 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 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 123 VAL 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 369 ASN Chi-restraints excluded: chain m residue 472 GLN Chi-restraints excluded: chain m residue 482 ARG 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 694 ASN 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 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 534 VAL 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 141 optimal weight: 0.9990 chunk 208 optimal weight: 5.9990 chunk 159 optimal weight: 0.7980 chunk 142 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 chunk 18 optimal weight: 0.9980 chunk 203 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 167 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 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** ** m 769 HIS ** 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 = 0.3679 r_free = 0.3679 target = 0.085152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.062324 restraints weight = 73210.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.064196 restraints weight = 40153.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.065403 restraints weight = 27666.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.066140 restraints weight = 21936.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.066568 restraints weight = 19072.179| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1761 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= 0.127 Angle : 0.583 13.641 24691 Z= 0.291 Chirality : 0.041 0.166 2735 Planarity : 0.003 0.061 3192 Dihedral : 4.170 27.840 2413 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.14 % Favored : 97.81 % Rotamer: Outliers : 3.40 % Allowed : 24.86 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.18), residues: 2193 helix: 1.93 (0.16), residues: 1059 sheet: -0.86 (0.26), residues: 373 loop : 0.02 (0.24), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG f 709 TYR 0.011 0.001 TYR o 502 PHE 0.018 0.001 PHE B 108 TRP 0.011 0.001 TRP o 483 HIS 0.014 0.001 HIS m 769 Details of bonding type rmsd covalent geometry : bond 0.00276 (18250) covalent geometry : angle 0.58269 (24691) hydrogen bonds : bond 0.04014 ( 978) hydrogen bonds : angle 4.20301 ( 2877) *********************** 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 250 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 184 time to evaluate : 0.753 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: 0.8328 (ttp80) cc_final: 0.7958 (ttp80) REVERT: B 98 LYS cc_start: 0.9369 (tppt) cc_final: 0.9161 (tppt) REVERT: B 107 LYS cc_start: 0.9381 (tmmt) cc_final: 0.8924 (tptt) REVERT: C 106 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8417 (mp0) REVERT: C 107 LYS cc_start: 0.9531 (ptpp) cc_final: 0.9192 (ptpp) REVERT: C 123 GLN cc_start: 0.9009 (tp-100) cc_final: 0.8758 (tp-100) REVERT: f 605 GLN cc_start: 0.8188 (tm-30) cc_final: 0.7907 (tm-30) REVERT: f 610 GLN cc_start: 0.8413 (tp40) cc_final: 0.7941 (tp40) REVERT: j 163 MET cc_start: 0.6968 (pmm) cc_final: 0.6663 (pmm) REVERT: j 277 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8143 (mp0) REVERT: j 289 HIS cc_start: 0.7939 (OUTLIER) cc_final: 0.7118 (t70) REVERT: m 622 LYS cc_start: 0.9427 (OUTLIER) cc_final: 0.9213 (ttmt) REVERT: m 691 MET cc_start: 0.9055 (tpp) cc_final: 0.8827 (tpp) REVERT: o 244 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.7583 (tm-30) REVERT: o 310 MET cc_start: 0.8501 (ptp) cc_final: 0.8256 (mtm) REVERT: o 445 MET cc_start: 0.8848 (tpp) cc_final: 0.8586 (tpp) REVERT: o 503 ASP cc_start: 0.8317 (m-30) cc_final: 0.7910 (m-30) outliers start: 66 outliers final: 41 residues processed: 236 average time/residue: 0.1472 time to fit residues: 51.7136 Evaluate side-chains 212 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 166 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 80 LEU 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 100 LEU 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 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 102 THR Chi-restraints excluded: chain j residue 134 ILE 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 j residue 349 VAL Chi-restraints excluded: chain m residue 339 PHE Chi-restraints excluded: chain m residue 472 GLN Chi-restraints excluded: chain m residue 482 ARG Chi-restraints excluded: chain m residue 484 LEU Chi-restraints excluded: chain m residue 577 ASN Chi-restraints excluded: chain m residue 622 LYS Chi-restraints excluded: chain m residue 694 ASN 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 63 optimal weight: 0.1980 chunk 24 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 187 optimal weight: 8.9990 chunk 170 optimal weight: 0.2980 chunk 57 optimal weight: 0.0050 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 GLN f 626 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** ** m 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 554 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.086119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.063536 restraints weight = 72391.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.065380 restraints weight = 40445.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.066546 restraints weight = 28158.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.067226 restraints weight = 22520.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.067678 restraints weight = 19763.098| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1921 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= 0.103 Angle : 0.580 13.860 24691 Z= 0.285 Chirality : 0.041 0.172 2735 Planarity : 0.003 0.041 3192 Dihedral : 3.974 33.329 2413 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.14 % Favored : 97.81 % Rotamer: Outliers : 3.29 % Allowed : 24.91 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.18), residues: 2193 helix: 2.04 (0.16), residues: 1064 sheet: -0.82 (0.26), residues: 373 loop : 0.07 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 84 TYR 0.009 0.001 TYR o 502 PHE 0.017 0.001 PHE m 843 TRP 0.010 0.001 TRP o 483 HIS 0.011 0.001 HIS m 769 Details of bonding type rmsd covalent geometry : bond 0.00218 (18250) covalent geometry : angle 0.57957 (24691) hydrogen bonds : bond 0.03809 ( 978) hydrogen bonds : angle 4.05102 ( 2877) *********************** 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 259 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 195 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 MET cc_start: 0.5874 (mpp) cc_final: 0.3528 (tpt) REVERT: B 107 LYS cc_start: 0.9375 (tmmt) cc_final: 0.8995 (tptt) REVERT: B 123 GLN cc_start: 0.9140 (tm-30) cc_final: 0.8587 (mt0) REVERT: C 106 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8454 (mp0) REVERT: C 107 LYS cc_start: 0.9499 (OUTLIER) cc_final: 0.9176 (ptpp) REVERT: C 123 GLN cc_start: 0.9026 (tp-100) cc_final: 0.8767 (tp-100) REVERT: f 605 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7888 (tm-30) REVERT: f 610 GLN cc_start: 0.8397 (tp40) cc_final: 0.7887 (tp40) REVERT: f 624 LYS cc_start: 0.9539 (mmmm) cc_final: 0.8917 (mmmm) REVERT: h 272 SER cc_start: 0.9435 (OUTLIER) cc_final: 0.9136 (p) REVERT: j 277 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8033 (mm-30) REVERT: j 289 HIS cc_start: 0.7957 (OUTLIER) cc_final: 0.7143 (t70) REVERT: m 413 MET cc_start: 0.9280 (ppp) cc_final: 0.8976 (ppp) REVERT: m 602 ARG cc_start: 0.8399 (mmm-85) cc_final: 0.8092 (mmm-85) REVERT: m 622 LYS cc_start: 0.9406 (OUTLIER) cc_final: 0.9181 (ttmt) REVERT: m 691 MET cc_start: 0.9092 (tpp) cc_final: 0.8862 (tpp) REVERT: o 244 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.7549 (tm-30) REVERT: o 310 MET cc_start: 0.8322 (ptp) cc_final: 0.8109 (mtm) REVERT: o 445 MET cc_start: 0.8815 (tpp) cc_final: 0.8325 (tpp) REVERT: o 503 ASP cc_start: 0.8348 (m-30) cc_final: 0.8049 (m-30) outliers start: 64 outliers final: 33 residues processed: 243 average time/residue: 0.1486 time to fit residues: 53.1454 Evaluate side-chains 212 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 78 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 100 LEU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain f residue 713 VAL 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 1040 VAL Chi-restraints excluded: chain h residue 272 SER 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 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 j residue 349 VAL Chi-restraints excluded: chain m residue 484 LEU Chi-restraints excluded: chain m residue 577 ASN Chi-restraints excluded: chain m residue 622 LYS Chi-restraints excluded: chain m residue 760 VAL Chi-restraints excluded: chain o residue 244 GLN 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 465 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 45 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 205 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 208 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 167 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 2 optimal weight: 0.0370 overall best weight: 1.2864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 GLN j 255 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** m 657 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.080766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.058839 restraints weight = 69039.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.060727 restraints weight = 35252.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.061913 restraints weight = 22978.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.062672 restraints weight = 17587.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.063115 restraints weight = 14919.763| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18250 Z= 0.119 Angle : 0.593 14.027 24691 Z= 0.291 Chirality : 0.041 0.175 2735 Planarity : 0.003 0.040 3192 Dihedral : 3.945 30.264 2413 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.46 % Favored : 97.49 % Rotamer: Outliers : 3.24 % Allowed : 25.68 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.18), residues: 2193 helix: 2.15 (0.16), residues: 1058 sheet: -0.86 (0.25), residues: 391 loop : 0.11 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 84 TYR 0.015 0.001 TYR B 94 PHE 0.017 0.001 PHE m 843 TRP 0.034 0.001 TRP m 755 HIS 0.009 0.001 HIS m 769 Details of bonding type rmsd covalent geometry : bond 0.00262 (18250) covalent geometry : angle 0.59349 (24691) hydrogen bonds : bond 0.03793 ( 978) hydrogen bonds : angle 4.03365 ( 2877) *********************** 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 247 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 184 time to evaluate : 0.715 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: 0.8288 (ttp80) cc_final: 0.7921 (ttp80) REVERT: B 107 LYS cc_start: 0.9389 (tmmt) cc_final: 0.9002 (tptt) REVERT: B 108 PHE cc_start: 0.9029 (t80) cc_final: 0.8010 (t80) REVERT: C 103 GLN cc_start: 0.9068 (mm-40) cc_final: 0.8861 (pp30) REVERT: C 107 LYS cc_start: 0.9475 (OUTLIER) cc_final: 0.9244 (pttm) REVERT: C 123 GLN cc_start: 0.8994 (tp-100) cc_final: 0.8738 (tp-100) REVERT: f 605 GLN cc_start: 0.8361 (tm-30) cc_final: 0.7970 (tm-30) REVERT: f 610 GLN cc_start: 0.8554 (tp40) cc_final: 0.7893 (tp40) REVERT: f 624 LYS cc_start: 0.9551 (mmmm) cc_final: 0.8919 (mmmm) REVERT: h 272 SER cc_start: 0.9419 (OUTLIER) cc_final: 0.9086 (p) REVERT: h 388 MET cc_start: 0.8395 (tpp) cc_final: 0.8041 (tpp) REVERT: j 163 MET cc_start: 0.6774 (pmm) cc_final: 0.6481 (pmm) REVERT: j 289 HIS cc_start: 0.7960 (OUTLIER) cc_final: 0.7080 (t70) REVERT: m 602 ARG cc_start: 0.8419 (mmm-85) cc_final: 0.8115 (mmm-85) REVERT: m 622 LYS cc_start: 0.9415 (OUTLIER) cc_final: 0.9155 (ttmt) REVERT: m 691 MET cc_start: 0.9150 (tpp) cc_final: 0.8925 (tpp) REVERT: o 244 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.7557 (tm-30) REVERT: o 310 MET cc_start: 0.8354 (ptp) cc_final: 0.8139 (mtm) REVERT: o 445 MET cc_start: 0.8975 (tpp) cc_final: 0.8532 (tpp) REVERT: o 503 ASP cc_start: 0.8393 (m-30) cc_final: 0.8039 (m-30) REVERT: o 567 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8156 (mp10) outliers start: 63 outliers final: 39 residues processed: 236 average time/residue: 0.1373 time to fit residues: 48.5358 Evaluate side-chains 221 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 176 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 58 LEU 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 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 C residue 107 LYS Chi-restraints excluded: chain f residue 713 VAL 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 1040 VAL Chi-restraints excluded: chain h residue 272 SER 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 550 VAL 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 289 HIS Chi-restraints excluded: chain m residue 339 PHE Chi-restraints excluded: chain m residue 577 ASN Chi-restraints excluded: chain m residue 622 LYS Chi-restraints excluded: chain m residue 760 VAL Chi-restraints excluded: chain o residue 244 GLN 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 436 HIS Chi-restraints excluded: chain o residue 465 VAL Chi-restraints excluded: chain o residue 567 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 51 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 121 optimal weight: 20.0000 chunk 212 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 171 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 135 optimal weight: 0.0980 chunk 115 optimal weight: 5.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- 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 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 255 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.080548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.058437 restraints weight = 70914.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.060226 restraints weight = 36848.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.061362 restraints weight = 24507.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.062083 restraints weight = 18987.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.062507 restraints weight = 16225.521| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18250 Z= 0.175 Angle : 0.623 13.513 24691 Z= 0.309 Chirality : 0.041 0.178 2735 Planarity : 0.003 0.039 3192 Dihedral : 4.026 29.159 2413 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.78 % Favored : 97.17 % Rotamer: Outliers : 3.14 % Allowed : 26.56 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.19), residues: 2193 helix: 2.16 (0.16), residues: 1059 sheet: -0.88 (0.26), residues: 379 loop : 0.17 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 84 TYR 0.015 0.001 TYR j 90 PHE 0.033 0.001 PHE C 111 TRP 0.020 0.001 TRP m 755 HIS 0.007 0.001 HIS m 769 Details of bonding type rmsd covalent geometry : bond 0.00387 (18250) covalent geometry : angle 0.62301 (24691) hydrogen bonds : bond 0.03846 ( 978) hydrogen bonds : angle 4.14996 ( 2877) *********************** 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 242 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 181 time to evaluate : 0.558 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: 0.8343 (ttp80) cc_final: 0.7973 (ttp80) REVERT: B 107 LYS cc_start: 0.9433 (tmmt) cc_final: 0.8986 (tptt) REVERT: B 123 GLN cc_start: 0.9152 (tm-30) cc_final: 0.8571 (mt0) REVERT: C 128 HIS cc_start: 0.4309 (OUTLIER) cc_final: 0.4009 (p-80) REVERT: f 605 GLN cc_start: 0.8407 (tm-30) cc_final: 0.8019 (tm-30) REVERT: f 610 GLN cc_start: 0.8523 (tp40) cc_final: 0.7832 (tp40) REVERT: f 624 LYS cc_start: 0.9565 (mmmm) cc_final: 0.8940 (mmmm) REVERT: h 272 SER cc_start: 0.9440 (OUTLIER) cc_final: 0.9102 (p) REVERT: j 163 MET cc_start: 0.6902 (pmm) cc_final: 0.6621 (pmm) REVERT: j 277 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8063 (mm-30) REVERT: j 289 HIS cc_start: 0.7900 (OUTLIER) cc_final: 0.7072 (t70) REVERT: m 413 MET cc_start: 0.9212 (ppp) cc_final: 0.8959 (ppp) REVERT: m 579 ASN cc_start: 0.8990 (m110) cc_final: 0.8664 (t0) REVERT: m 602 ARG cc_start: 0.8472 (mmm-85) cc_final: 0.8132 (mmm-85) REVERT: m 622 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.9189 (ttmt) REVERT: m 691 MET cc_start: 0.9133 (tpp) cc_final: 0.8932 (tpp) REVERT: o 244 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.7610 (tm-30) REVERT: o 503 ASP cc_start: 0.8370 (m-30) cc_final: 0.7996 (m-30) REVERT: o 548 ASN cc_start: 0.9126 (t0) cc_final: 0.8764 (t0) outliers start: 61 outliers final: 46 residues processed: 231 average time/residue: 0.1401 time to fit residues: 47.8481 Evaluate side-chains 222 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 170 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 58 LEU 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 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 C residue 106 GLU Chi-restraints excluded: chain C residue 128 HIS Chi-restraints excluded: chain f residue 608 LEU Chi-restraints excluded: chain f residue 713 VAL 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 857 ILE Chi-restraints excluded: chain f residue 888 LEU Chi-restraints excluded: chain f residue 1040 VAL Chi-restraints excluded: chain h residue 272 SER 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 550 VAL Chi-restraints excluded: chain j residue 90 TYR 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 339 PHE Chi-restraints excluded: chain m residue 369 ASN Chi-restraints excluded: chain m residue 577 ASN Chi-restraints excluded: chain m residue 622 LYS 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 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 465 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 153 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 chunk 197 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 187 optimal weight: 0.6980 chunk 188 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 96 optimal weight: 0.0870 overall best weight: 1.1162 ------------------------------------------------------------------------------- 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** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.081866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.059666 restraints weight = 70192.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.061498 restraints weight = 36238.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.062658 restraints weight = 23915.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.063391 restraints weight = 18471.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.063831 restraints weight = 15771.069| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18250 Z= 0.118 Angle : 0.622 15.039 24691 Z= 0.301 Chirality : 0.041 0.203 2735 Planarity : 0.003 0.039 3192 Dihedral : 3.911 23.980 2413 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.83 % Allowed : 26.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.19), residues: 2193 helix: 2.18 (0.16), residues: 1062 sheet: -0.84 (0.26), residues: 391 loop : 0.23 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 84 TYR 0.010 0.001 TYR o 431 PHE 0.020 0.001 PHE C 111 TRP 0.017 0.001 TRP m 755 HIS 0.007 0.001 HIS m 769 Details of bonding type rmsd covalent geometry : bond 0.00263 (18250) covalent geometry : angle 0.62164 (24691) hydrogen bonds : bond 0.03743 ( 978) hydrogen bonds : angle 4.04209 ( 2877) *********************** 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 239 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 184 time to evaluate : 0.721 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: 0.8275 (ttp80) cc_final: 0.7886 (ttp80) REVERT: B 98 LYS cc_start: 0.9237 (tppt) cc_final: 0.8863 (tppt) REVERT: B 107 LYS cc_start: 0.9413 (tmmt) cc_final: 0.8966 (tptt) REVERT: f 605 GLN cc_start: 0.8421 (tm-30) cc_final: 0.8038 (tm-30) REVERT: f 610 GLN cc_start: 0.8530 (tp40) cc_final: 0.7834 (tp40) REVERT: f 624 LYS cc_start: 0.9554 (mmmm) cc_final: 0.8926 (mmmm) REVERT: h 272 SER cc_start: 0.9400 (OUTLIER) cc_final: 0.9063 (p) REVERT: h 445 MET cc_start: 0.8299 (tpt) cc_final: 0.7921 (tpt) REVERT: j 163 MET cc_start: 0.6832 (pmm) cc_final: 0.6561 (pmm) REVERT: j 277 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8078 (mm-30) REVERT: j 289 HIS cc_start: 0.7889 (OUTLIER) cc_final: 0.7011 (t70) REVERT: m 413 MET cc_start: 0.9197 (ppp) cc_final: 0.8856 (ppp) REVERT: m 579 ASN cc_start: 0.8952 (m110) cc_final: 0.8640 (t0) REVERT: m 602 ARG cc_start: 0.8394 (mmm-85) cc_final: 0.8074 (mmm-85) REVERT: m 622 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.9166 (ttmt) REVERT: m 691 MET cc_start: 0.9122 (tpp) cc_final: 0.8918 (tpp) REVERT: o 244 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.7594 (tm-30) REVERT: o 503 ASP cc_start: 0.8327 (m-30) cc_final: 0.7918 (m-30) REVERT: o 548 ASN cc_start: 0.9064 (t0) cc_final: 0.8416 (t0) outliers start: 55 outliers final: 41 residues processed: 228 average time/residue: 0.1531 time to fit residues: 51.4523 Evaluate side-chains 223 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 177 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LEU 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 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 C residue 106 GLU Chi-restraints excluded: chain f residue 713 VAL 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 857 ILE Chi-restraints excluded: chain f residue 888 LEU Chi-restraints excluded: chain f residue 1040 VAL Chi-restraints excluded: chain h residue 272 SER 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 h residue 573 VAL Chi-restraints excluded: chain j residue 90 TYR 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 339 PHE Chi-restraints excluded: chain m residue 577 ASN Chi-restraints excluded: chain m residue 622 LYS 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 415 VAL 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 75 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 176 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 91 optimal weight: 0.0170 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- 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** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.081963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.059782 restraints weight = 70014.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.061642 restraints weight = 36101.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.062807 restraints weight = 23763.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.063526 restraints weight = 18355.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.063892 restraints weight = 15711.009| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2285 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= 0.118 Angle : 0.630 15.335 24691 Z= 0.305 Chirality : 0.041 0.216 2735 Planarity : 0.003 0.039 3192 Dihedral : 3.872 20.469 2413 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.73 % Allowed : 26.76 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.19), residues: 2193 helix: 2.13 (0.16), residues: 1069 sheet: -0.82 (0.25), residues: 401 loop : 0.27 (0.25), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 96 TYR 0.012 0.001 TYR h 502 PHE 0.023 0.001 PHE B 108 TRP 0.014 0.001 TRP m 755 HIS 0.007 0.001 HIS m 769 Details of bonding type rmsd covalent geometry : bond 0.00265 (18250) covalent geometry : angle 0.63035 (24691) hydrogen bonds : bond 0.03700 ( 978) hydrogen bonds : angle 4.02793 ( 2877) *********************** 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 239 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 186 time to evaluate : 0.636 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 84 ARG cc_start: 0.8359 (mtt180) cc_final: 0.8101 (mtt90) REVERT: B 85 GLU cc_start: 0.9032 (tm-30) cc_final: 0.8625 (tm-30) REVERT: B 96 ARG cc_start: 0.8231 (ttp80) cc_final: 0.7841 (ttp80) REVERT: B 98 LYS cc_start: 0.9235 (tppt) cc_final: 0.8919 (tppt) REVERT: B 107 LYS cc_start: 0.9409 (tmmt) cc_final: 0.8964 (tptt) REVERT: C 128 HIS cc_start: 0.4725 (OUTLIER) cc_final: 0.4365 (p-80) REVERT: f 605 GLN cc_start: 0.8448 (tm-30) cc_final: 0.8066 (tm-30) REVERT: f 610 GLN cc_start: 0.8531 (tp40) cc_final: 0.7805 (tp40) REVERT: f 624 LYS cc_start: 0.9549 (mmmm) cc_final: 0.8964 (mmmm) REVERT: h 272 SER cc_start: 0.9402 (OUTLIER) cc_final: 0.9060 (p) REVERT: h 445 MET cc_start: 0.8298 (tpt) cc_final: 0.7869 (tpt) REVERT: j 107 TRP cc_start: 0.8936 (m100) cc_final: 0.8448 (m100) REVERT: j 163 MET cc_start: 0.6787 (pmm) cc_final: 0.6522 (pmm) REVERT: j 277 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8063 (mm-30) REVERT: j 289 HIS cc_start: 0.7930 (OUTLIER) cc_final: 0.7060 (t70) REVERT: m 602 ARG cc_start: 0.8367 (mmm-85) cc_final: 0.8070 (mmm-85) REVERT: m 622 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.9144 (ttmt) REVERT: o 244 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.7556 (tm-30) REVERT: o 503 ASP cc_start: 0.8401 (m-30) cc_final: 0.8017 (m-30) REVERT: o 548 ASN cc_start: 0.9058 (t0) cc_final: 0.8427 (t0) REVERT: o 567 GLN cc_start: 0.8564 (pm20) cc_final: 0.8121 (mp10) outliers start: 53 outliers final: 40 residues processed: 228 average time/residue: 0.1451 time to fit residues: 48.6138 Evaluate side-chains 228 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 182 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 LEU 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 100 LEU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 128 HIS Chi-restraints excluded: chain f residue 713 VAL 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 857 ILE Chi-restraints excluded: chain f residue 888 LEU Chi-restraints excluded: chain f residue 1040 VAL Chi-restraints excluded: chain h residue 272 SER 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 550 VAL Chi-restraints excluded: chain h residue 573 VAL Chi-restraints excluded: chain j residue 90 TYR 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 339 PHE Chi-restraints excluded: chain m residue 577 ASN Chi-restraints excluded: chain m residue 622 LYS 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 415 VAL 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 133 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 78 optimal weight: 0.0070 chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 overall best weight: 3.0006 ------------------------------------------------------------------------------- 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 123 GLN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.080197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.058817 restraints weight = 70437.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.060592 restraints weight = 35814.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.061711 restraints weight = 23510.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.062410 restraints weight = 18139.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.062827 restraints weight = 15458.969| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 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 : 0.004 0.056 18250 Z= 0.197 Angle : 0.672 14.882 24691 Z= 0.331 Chirality : 0.042 0.222 2735 Planarity : 0.004 0.039 3192 Dihedral : 4.053 23.522 2413 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.96 % Favored : 96.99 % Rotamer: Outliers : 2.52 % Allowed : 27.28 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.19), residues: 2193 helix: 2.04 (0.16), residues: 1069 sheet: -0.87 (0.26), residues: 379 loop : 0.30 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG f1003 TYR 0.013 0.001 TYR o 502 PHE 0.018 0.001 PHE C 111 TRP 0.020 0.001 TRP m 423 HIS 0.006 0.001 HIS m 473 Details of bonding type rmsd covalent geometry : bond 0.00436 (18250) covalent geometry : angle 0.67181 (24691) hydrogen bonds : bond 0.03867 ( 978) hydrogen bonds : angle 4.18190 ( 2877) ********************** 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 228 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 179 time to evaluate : 0.715 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 85 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8657 (tm-30) REVERT: B 96 ARG cc_start: 0.8321 (ttp80) cc_final: 0.7927 (ttp80) REVERT: B 107 LYS cc_start: 0.9385 (tmmt) cc_final: 0.8966 (tptt) REVERT: C 128 HIS cc_start: 0.4537 (OUTLIER) cc_final: 0.4191 (p-80) REVERT: f 605 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8135 (tm-30) REVERT: f 610 GLN cc_start: 0.8557 (tp40) cc_final: 0.8084 (tp40) REVERT: f 624 LYS cc_start: 0.9572 (mmmm) cc_final: 0.8955 (mmmm) REVERT: f 663 LYS cc_start: 0.8993 (tppt) cc_final: 0.8719 (tppt) REVERT: h 445 MET cc_start: 0.8386 (tpt) cc_final: 0.8052 (tpt) REVERT: j 289 HIS cc_start: 0.7932 (OUTLIER) cc_final: 0.7097 (t70) REVERT: m 413 MET cc_start: 0.9274 (ppp) cc_final: 0.9062 (ppp) REVERT: m 579 ASN cc_start: 0.8984 (m110) cc_final: 0.8687 (t0) REVERT: m 602 ARG cc_start: 0.8467 (mmm-85) cc_final: 0.8139 (mmm-85) REVERT: o 244 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.7609 (tm-30) REVERT: o 503 ASP cc_start: 0.8414 (m-30) cc_final: 0.7991 (m-30) REVERT: o 548 ASN cc_start: 0.9169 (t0) cc_final: 0.8754 (t0) outliers start: 49 outliers final: 43 residues processed: 217 average time/residue: 0.1462 time to fit residues: 46.6170 Evaluate side-chains 218 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 172 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 58 LEU 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 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 C residue 106 GLU Chi-restraints excluded: chain C residue 128 HIS Chi-restraints excluded: chain f residue 713 VAL Chi-restraints excluded: chain f residue 755 TRP Chi-restraints excluded: chain f residue 845 GLU Chi-restraints excluded: chain f residue 857 ILE Chi-restraints excluded: chain f residue 888 LEU 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 550 VAL Chi-restraints excluded: chain h residue 573 VAL Chi-restraints excluded: chain j residue 90 TYR 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 289 HIS Chi-restraints excluded: chain m residue 369 ASN 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 269 LEU 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 465 VAL Chi-restraints excluded: chain o residue 534 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 208 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 87 optimal weight: 0.0170 chunk 161 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 213 optimal weight: 0.9980 chunk 171 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 211 optimal weight: 1.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- 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** j 255 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.081966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.059795 restraints weight = 70020.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.061658 restraints weight = 36058.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.062829 restraints weight = 23763.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.063537 restraints weight = 18363.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.063908 restraints weight = 15713.869| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18250 Z= 0.115 Angle : 0.651 15.704 24691 Z= 0.315 Chirality : 0.041 0.225 2735 Planarity : 0.003 0.038 3192 Dihedral : 3.902 19.937 2413 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.47 % Allowed : 27.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.19), residues: 2193 helix: 2.08 (0.16), residues: 1076 sheet: -0.78 (0.26), residues: 391 loop : 0.30 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG j 171 TYR 0.008 0.001 TYR h 502 PHE 0.034 0.001 PHE B 108 TRP 0.020 0.001 TRP m 423 HIS 0.006 0.001 HIS m 769 Details of bonding type rmsd covalent geometry : bond 0.00257 (18250) covalent geometry : angle 0.65065 (24691) hydrogen bonds : bond 0.03728 ( 978) hydrogen bonds : angle 4.04301 ( 2877) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2857.03 seconds wall clock time: 50 minutes 28.50 seconds (3028.50 seconds total)