Starting phenix.real_space_refine on Thu Jul 31 16:23:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jmn_22397/07_2025/7jmn_22397.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jmn_22397/07_2025/7jmn_22397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jmn_22397/07_2025/7jmn_22397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jmn_22397/07_2025/7jmn_22397.map" model { file = "/net/cci-nas-00/data/ceres_data/7jmn_22397/07_2025/7jmn_22397.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jmn_22397/07_2025/7jmn_22397.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.037 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 62 5.16 5 C 8610 2.51 5 N 2391 2.21 5 O 2570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13633 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 4467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4467 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 34, 'TRANS': 549} Chain breaks: 8 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 40 Chain: "N" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1439 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 44} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 103 Chain: "P" Number of atoms: 6178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 810, 6178 Classifications: {'peptide': 810} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 49, 'TRANS': 760} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'TRP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 71 Chain: "O" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1290 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 156} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Chain: "X" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 259 Classifications: {'peptide': 52} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 51} Link IDs: {'TRANS': 51} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 52} Unresolved non-hydrogen planarities: 52 Time building chain proxies: 10.21, per 1000 atoms: 0.75 Number of scatterers: 13633 At special positions: 0 Unit cell: (162.208, 164.4, 104.12, 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 62 16.00 O 2570 8.00 N 2391 7.00 C 8610 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: 3.20 Conformation dependent library (CDL) restraints added in 2.0 seconds 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3420 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 13 sheets defined 37.8% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'E' and resid 69 through 82 removed outlier: 3.714A pdb=" N TYR E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 230 removed outlier: 4.364A pdb=" N GLU E 225 " --> pdb=" O PHE E 221 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASN E 226 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN E 227 " --> pdb=" O PHE E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 249 removed outlier: 4.034A pdb=" N ILE E 241 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS E 242 " --> pdb=" O CYS E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 324 Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 352 through 361 removed outlier: 3.880A pdb=" N LEU E 361 " --> pdb=" O ALA E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 391 removed outlier: 4.327A pdb=" N ILE E 383 " --> pdb=" O LYS E 379 " (cutoff:3.500A) Proline residue: E 387 - end of helix Processing helix chain 'E' and resid 397 through 405 removed outlier: 4.830A pdb=" N TYR E 402 " --> pdb=" O THR E 399 " (cutoff:3.500A) Proline residue: E 403 - end of helix Processing helix chain 'E' and resid 441 through 446 removed outlier: 3.897A pdb=" N CYS E 446 " --> pdb=" O ARG E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 482 removed outlier: 3.652A pdb=" N GLU E 481 " --> pdb=" O TYR E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 510 Processing helix chain 'E' and resid 515 through 524 removed outlier: 3.864A pdb=" N SER E 524 " --> pdb=" O ARG E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 528 Processing helix chain 'E' and resid 529 through 536 removed outlier: 3.960A pdb=" N LEU E 533 " --> pdb=" O LEU E 529 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE E 535 " --> pdb=" O VAL E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 541 removed outlier: 3.654A pdb=" N LYS E 540 " --> pdb=" O LYS E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 550 removed outlier: 3.697A pdb=" N GLU E 547 " --> pdb=" O HIS E 543 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LEU E 548 " --> pdb=" O PRO E 544 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU E 549 " --> pdb=" O LEU E 545 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP E 550 " --> pdb=" O CYS E 546 " (cutoff:3.500A) Processing helix chain 'E' and resid 563 through 583 removed outlier: 3.814A pdb=" N GLU E 567 " --> pdb=" O GLN E 563 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL E 572 " --> pdb=" O GLU E 568 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU E 575 " --> pdb=" O SER E 571 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU E 576 " --> pdb=" O VAL E 572 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU E 577 " --> pdb=" O LEU E 573 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA E 578 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR E 581 " --> pdb=" O LEU E 577 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR E 583 " --> pdb=" O PHE E 579 " (cutoff:3.500A) Processing helix chain 'E' and resid 606 through 613 Proline residue: E 611 - end of helix Processing helix chain 'E' and resid 655 through 668 removed outlier: 3.650A pdb=" N ALA E 668 " --> pdb=" O ASN E 664 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 681 Processing helix chain 'E' and resid 688 through 690 No H-bonds generated for 'chain 'E' and resid 688 through 690' Processing helix chain 'E' and resid 691 through 699 removed outlier: 3.750A pdb=" N ALA E 695 " --> pdb=" O ALA E 691 " (cutoff:3.500A) Processing helix chain 'E' and resid 707 through 718 Processing helix chain 'E' and resid 718 through 723 removed outlier: 3.758A pdb=" N LEU E 722 " --> pdb=" O LEU E 718 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS E 723 " --> pdb=" O GLN E 719 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 718 through 723' Processing helix chain 'E' and resid 728 through 757 removed outlier: 4.230A pdb=" N ASN E 740 " --> pdb=" O SER E 736 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE E 741 " --> pdb=" O SER E 737 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL E 742 " --> pdb=" O VAL E 738 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LYS E 744 " --> pdb=" O ASN E 740 " (cutoff:3.500A) Proline residue: E 745 - end of helix removed outlier: 4.070A pdb=" N HIS E 748 " --> pdb=" O LYS E 744 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ALA E 749 " --> pdb=" O PRO E 745 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU E 750 " --> pdb=" O LEU E 746 " (cutoff:3.500A) Processing helix chain 'E' and resid 763 through 769 removed outlier: 3.628A pdb=" N LEU E 767 " --> pdb=" O ILE E 763 " (cutoff:3.500A) Processing helix chain 'E' and resid 784 through 789 Processing helix chain 'E' and resid 843 through 851 removed outlier: 4.241A pdb=" N GLN E 849 " --> pdb=" O LEU E 845 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE E 850 " --> pdb=" O ALA E 846 " (cutoff:3.500A) Processing helix chain 'E' and resid 852 through 867 removed outlier: 3.611A pdb=" N SER E 866 " --> pdb=" O ASP E 862 " (cutoff:3.500A) Processing helix chain 'E' and resid 874 through 882 Processing helix chain 'N' and resid 800 through 813 removed outlier: 4.156A pdb=" N GLN N 805 " --> pdb=" O ILE N 801 " (cutoff:3.500A) Processing helix chain 'N' and resid 814 through 819 removed outlier: 3.941A pdb=" N ARG N 818 " --> pdb=" O GLU N 814 " (cutoff:3.500A) Processing helix chain 'N' and resid 876 through 880 removed outlier: 3.677A pdb=" N ARG N 880 " --> pdb=" O VAL N 877 " (cutoff:3.500A) Processing helix chain 'N' and resid 882 through 889 removed outlier: 3.971A pdb=" N ASN N 886 " --> pdb=" O GLU N 882 " (cutoff:3.500A) Processing helix chain 'N' and resid 896 through 914 Proline residue: N 902 - end of helix Processing helix chain 'N' and resid 914 through 920 removed outlier: 3.861A pdb=" N GLN N 918 " --> pdb=" O TRP N 914 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU N 919 " --> pdb=" O GLN N 915 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN N 920 " --> pdb=" O THR N 916 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 914 through 920' Processing helix chain 'N' and resid 978 through 983 Processing helix chain 'N' and resid 995 through 1012 removed outlier: 4.369A pdb=" N GLY N 999 " --> pdb=" O SER N 995 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA N1006 " --> pdb=" O THR N1002 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU N1007 " --> pdb=" O GLY N1003 " (cutoff:3.500A) Proline residue: N1008 - end of helix Processing helix chain 'P' and resid 210 through 213 removed outlier: 4.118A pdb=" N VAL P 213 " --> pdb=" O HIS P 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 210 through 213' Processing helix chain 'P' and resid 563 through 568 removed outlier: 4.096A pdb=" N LYS P 566 " --> pdb=" O GLN P 563 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU P 567 " --> pdb=" O GLY P 564 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS P 568 " --> pdb=" O PRO P 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 563 through 568' Processing helix chain 'P' and resid 569 through 575 removed outlier: 3.907A pdb=" N SER P 573 " --> pdb=" O ALA P 569 " (cutoff:3.500A) Processing helix chain 'P' and resid 607 through 615 removed outlier: 3.884A pdb=" N THR P 611 " --> pdb=" O LYS P 607 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA P 612 " --> pdb=" O ASP P 608 " (cutoff:3.500A) Processing helix chain 'P' and resid 637 through 641 Processing helix chain 'P' and resid 654 through 672 removed outlier: 3.920A pdb=" N GLN P 659 " --> pdb=" O ASN P 655 " (cutoff:3.500A) Proline residue: P 660 - end of helix removed outlier: 4.281A pdb=" N LYS P 666 " --> pdb=" O THR P 662 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASN P 669 " --> pdb=" O GLY P 665 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LEU P 670 " --> pdb=" O LYS P 666 " (cutoff:3.500A) Processing helix chain 'P' and resid 699 through 726 removed outlier: 3.642A pdb=" N VAL P 703 " --> pdb=" O ASP P 699 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL P 704 " --> pdb=" O GLU P 700 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ASP P 705 " --> pdb=" O PRO P 701 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA P 706 " --> pdb=" O GLU P 702 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP P 713 " --> pdb=" O SER P 709 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU P 726 " --> pdb=" O THR P 722 " (cutoff:3.500A) Processing helix chain 'P' and resid 742 through 751 removed outlier: 3.970A pdb=" N TYR P 750 " --> pdb=" O ASP P 746 " (cutoff:3.500A) Processing helix chain 'P' and resid 763 through 790 removed outlier: 3.885A pdb=" N GLY P 769 " --> pdb=" O SER P 765 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA P 773 " --> pdb=" O GLY P 769 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL P 780 " --> pdb=" O ARG P 776 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL P 781 " --> pdb=" O ARG P 777 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU P 782 " --> pdb=" O LEU P 778 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER P 783 " --> pdb=" O GLN P 779 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG P 787 " --> pdb=" O SER P 783 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA P 788 " --> pdb=" O LEU P 784 " (cutoff:3.500A) Processing helix chain 'P' and resid 827 through 838 removed outlier: 4.107A pdb=" N ASP P 833 " --> pdb=" O ALA P 829 " (cutoff:3.500A) Processing helix chain 'P' and resid 850 through 868 removed outlier: 4.582A pdb=" N THR P 856 " --> pdb=" O SER P 852 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN P 857 " --> pdb=" O GLY P 853 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N HIS P 861 " --> pdb=" O GLN P 857 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA P 862 " --> pdb=" O ILE P 858 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER P 863 " --> pdb=" O ARG P 859 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY P 866 " --> pdb=" O ALA P 862 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN P 868 " --> pdb=" O GLY P 864 " (cutoff:3.500A) Processing helix chain 'P' and resid 890 through 899 Processing helix chain 'P' and resid 923 through 927 removed outlier: 3.572A pdb=" N SER P 927 " --> pdb=" O ASP P 924 " (cutoff:3.500A) Processing helix chain 'P' and resid 937 through 942 removed outlier: 3.569A pdb=" N VAL P 940 " --> pdb=" O GLU P 937 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA P 941 " --> pdb=" O GLU P 938 " (cutoff:3.500A) Processing helix chain 'P' and resid 948 through 952 Processing helix chain 'O' and resid 89 through 104 removed outlier: 4.955A pdb=" N LEU O 95 " --> pdb=" O ALA O 91 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLU O 98 " --> pdb=" O ALA O 94 " (cutoff:3.500A) Processing helix chain 'O' and resid 105 through 111 Processing helix chain 'O' and resid 134 through 147 Processing helix chain 'O' and resid 148 through 159 removed outlier: 3.845A pdb=" N GLN O 152 " --> pdb=" O GLN O 148 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG O 159 " --> pdb=" O GLN O 155 " (cutoff:3.500A) Processing helix chain 'O' and resid 165 through 170 Processing helix chain 'O' and resid 252 through 259 Processing helix chain 'O' and resid 262 through 270 removed outlier: 4.377A pdb=" N GLN O 268 " --> pdb=" O ARG O 264 " (cutoff:3.500A) Processing helix chain 'O' and resid 280 through 284 removed outlier: 3.708A pdb=" N GLY O 283 " --> pdb=" O ASN O 280 " (cutoff:3.500A) Processing helix chain 'O' and resid 287 through 311 removed outlier: 4.162A pdb=" N GLN O 297 " --> pdb=" O ASN O 293 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE O 299 " --> pdb=" O VAL O 295 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N THR O 302 " --> pdb=" O VAL O 298 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N MET O 303 " --> pdb=" O PHE O 299 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU O 304 " --> pdb=" O ARG O 300 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU O 308 " --> pdb=" O LEU O 304 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS O 309 " --> pdb=" O GLN O 305 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN O 311 " --> pdb=" O GLN O 307 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'N' and resid 852 through 854 removed outlier: 4.247A pdb=" N LEU N 868 " --> pdb=" O ASP N 854 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 924 through 927 Processing sheet with id=AA3, first strand: chain 'N' and resid 962 through 963 Processing sheet with id=AA4, first strand: chain 'P' and resid 93 through 97 removed outlier: 3.699A pdb=" N VAL P 151 " --> pdb=" O ALA P 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 158 through 163 removed outlier: 3.574A pdb=" N GLU P 173 " --> pdb=" O PHE P 186 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE P 185 " --> pdb=" O SER P 198 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 215 through 217 Processing sheet with id=AA7, first strand: chain 'P' and resid 227 through 232 Processing sheet with id=AA8, first strand: chain 'P' and resid 299 through 305 removed outlier: 3.765A pdb=" N ILE P 299 " --> pdb=" O SER P 314 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA P 309 " --> pdb=" O GLN P 325 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN P 325 " --> pdb=" O ALA P 309 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N VAL P 322 " --> pdb=" O GLY P 366 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLY P 366 " --> pdb=" O VAL P 322 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 395 through 396 removed outlier: 3.769A pdb=" N ALA P 410 " --> pdb=" O LEU P 396 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'P' and resid 438 through 442 removed outlier: 3.562A pdb=" N LEU P 439 " --> pdb=" O GLN P 453 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 527 through 530 removed outlier: 3.719A pdb=" N GLN P 527 " --> pdb=" O VAL P 540 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE P 537 " --> pdb=" O VAL P 549 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 956 through 958 Processing sheet with id=AB4, first strand: chain 'X' and resid 66 through 68 368 hydrogen bonds defined for protein. 1020 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.51 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4601 1.34 - 1.46: 2675 1.46 - 1.58: 6517 1.58 - 1.70: 0 1.70 - 1.82: 92 Bond restraints: 13885 Sorted by residual: bond pdb=" N ASP P 556 " pdb=" CA ASP P 556 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.85e+00 bond pdb=" CA VAL E 606 " pdb=" CB VAL E 606 " ideal model delta sigma weight residual 1.551 1.532 0.018 1.08e-02 8.57e+03 2.91e+00 bond pdb=" CA GLY N 800 " pdb=" C GLY N 800 " ideal model delta sigma weight residual 1.513 1.527 -0.014 1.06e-02 8.90e+03 1.86e+00 bond pdb=" C THR O 272 " pdb=" N PRO O 273 " ideal model delta sigma weight residual 1.339 1.384 -0.044 3.40e-02 8.65e+02 1.71e+00 bond pdb=" C PHE P 916 " pdb=" N PRO P 917 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.30e-02 5.92e+03 1.56e+00 ... (remaining 13880 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 18599 2.80 - 5.59: 269 5.59 - 8.39: 26 8.39 - 11.19: 3 11.19 - 13.99: 1 Bond angle restraints: 18898 Sorted by residual: angle pdb=" N PRO E 254 " pdb=" CA PRO E 254 " pdb=" CB PRO E 254 " ideal model delta sigma weight residual 103.25 111.61 -8.36 1.05e+00 9.07e-01 6.34e+01 angle pdb=" N PRO P 380 " pdb=" CA PRO P 380 " pdb=" CB PRO P 380 " ideal model delta sigma weight residual 103.25 111.18 -7.93 1.05e+00 9.07e-01 5.71e+01 angle pdb=" N PRO P 869 " pdb=" CA PRO P 869 " pdb=" CB PRO P 869 " ideal model delta sigma weight residual 103.25 111.08 -7.83 1.05e+00 9.07e-01 5.56e+01 angle pdb=" N PRO E 305 " pdb=" CA PRO E 305 " pdb=" CB PRO E 305 " ideal model delta sigma weight residual 103.25 111.07 -7.82 1.05e+00 9.07e-01 5.55e+01 angle pdb=" N PRO O 188 " pdb=" CA PRO O 188 " pdb=" CB PRO O 188 " ideal model delta sigma weight residual 102.86 110.55 -7.69 1.23e+00 6.61e-01 3.91e+01 ... (remaining 18893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 7457 17.48 - 34.96: 773 34.96 - 52.44: 125 52.44 - 69.93: 20 69.93 - 87.41: 12 Dihedral angle restraints: 8387 sinusoidal: 3141 harmonic: 5246 Sorted by residual: dihedral pdb=" CA GLY P 487 " pdb=" C GLY P 487 " pdb=" N THR P 488 " pdb=" CA THR P 488 " ideal model delta harmonic sigma weight residual 180.00 151.69 28.31 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA LEU E 472 " pdb=" C LEU E 472 " pdb=" N PRO E 473 " pdb=" CA PRO E 473 " ideal model delta harmonic sigma weight residual 180.00 152.22 27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA PRO P 271 " pdb=" C PRO P 271 " pdb=" N GLN P 272 " pdb=" CA GLN P 272 " ideal model delta harmonic sigma weight residual 180.00 153.33 26.67 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 8384 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1727 0.055 - 0.110: 411 0.110 - 0.165: 54 0.165 - 0.220: 7 0.220 - 0.276: 4 Chirality restraints: 2203 Sorted by residual: chirality pdb=" CA PRO E 254 " pdb=" N PRO E 254 " pdb=" C PRO E 254 " pdb=" CB PRO E 254 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA ASN P 899 " pdb=" N ASN P 899 " pdb=" C ASN P 899 " pdb=" CB ASN P 899 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA PRO P 380 " pdb=" N PRO P 380 " pdb=" C PRO P 380 " pdb=" CB PRO P 380 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 2200 not shown) Planarity restraints: 2478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 791 " 0.030 2.00e-02 2.50e+03 2.39e-02 1.43e+01 pdb=" CG TRP E 791 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP E 791 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP E 791 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 791 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 791 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 791 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 791 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 791 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP E 791 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU O 95 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.50e+00 pdb=" C LEU O 95 " -0.044 2.00e-02 2.50e+03 pdb=" O LEU O 95 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN O 96 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN P 899 " 0.042 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO P 900 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO P 900 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO P 900 " 0.035 5.00e-02 4.00e+02 ... (remaining 2475 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 311 2.67 - 3.23: 13340 3.23 - 3.79: 17977 3.79 - 4.34: 23283 4.34 - 4.90: 38487 Nonbonded interactions: 93398 Sorted by model distance: nonbonded pdb=" OH TYR E 402 " pdb=" OG SER E 456 " model vdw 2.115 3.040 nonbonded pdb=" OD1 ASP E 530 " pdb=" OH TYR E 583 " model vdw 2.149 3.040 nonbonded pdb=" NE2 GLN P 413 " pdb=" OE1 GLN P 438 " model vdw 2.188 3.120 nonbonded pdb=" NZ LYS P 607 " pdb=" O GLN P 635 " model vdw 2.230 3.120 nonbonded pdb=" OE1 GLN O 268 " pdb=" OG SER O 282 " model vdw 2.237 3.040 ... (remaining 93393 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 7.040 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: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 33.470 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 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 : 0.004 0.053 13885 Z= 0.183 Angle : 0.828 13.987 18898 Z= 0.462 Chirality : 0.048 0.276 2203 Planarity : 0.005 0.062 2478 Dihedral : 14.636 87.407 4967 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.58 % Allowed : 19.25 % Favored : 80.16 % Rotamer: Outliers : 0.07 % Allowed : 9.67 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.81 (0.16), residues: 1714 helix: -3.09 (0.16), residues: 616 sheet: -2.81 (0.35), residues: 175 loop : -4.85 (0.16), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP E 791 HIS 0.006 0.001 HIS E 340 PHE 0.020 0.002 PHE E 404 TYR 0.017 0.001 TYR E 343 ARG 0.010 0.000 ARG E 243 Details of bonding type rmsd hydrogen bonds : bond 0.11083 ( 368) hydrogen bonds : angle 5.42784 ( 1020) covalent geometry : bond 0.00384 (13885) covalent geometry : angle 0.82830 (18898) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 219 PHE cc_start: 0.7552 (p90) cc_final: 0.6881 (p90) REVERT: N 870 LYS cc_start: 0.8214 (mtpt) cc_final: 0.7900 (mmmt) REVERT: N 880 ARG cc_start: 0.6938 (mmt180) cc_final: 0.6396 (mmt90) REVERT: P 201 TRP cc_start: 0.8027 (p-90) cc_final: 0.7753 (p-90) REVERT: P 408 LEU cc_start: 0.8677 (pp) cc_final: 0.8437 (pp) REVERT: P 436 PHE cc_start: 0.6901 (m-80) cc_final: 0.6401 (m-80) REVERT: P 491 TYR cc_start: 0.6858 (t80) cc_final: 0.6617 (t80) REVERT: P 768 ARG cc_start: 0.8481 (ptp-110) cc_final: 0.8035 (ppt170) REVERT: P 904 PHE cc_start: 0.8275 (m-80) cc_final: 0.8006 (m-80) REVERT: O 144 GLN cc_start: 0.7911 (mt0) cc_final: 0.7556 (tt0) REVERT: O 264 ARG cc_start: 0.7739 (mtt180) cc_final: 0.7430 (ttm170) REVERT: O 309 LYS cc_start: 0.8196 (mttt) cc_final: 0.7979 (mttm) outliers start: 1 outliers final: 1 residues processed: 226 average time/residue: 0.3326 time to fit residues: 102.3755 Evaluate side-chains 181 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 644 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 151 optimal weight: 0.3980 chunk 135 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 140 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 85 optimal weight: 0.0040 chunk 104 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 344 GLN E 485 GLN E 543 HIS E 618 GLN N 872 ASN N 879 ASN N 935 HIS P 168 HIS P 190 GLN ** P 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 274 ASN P 275 ASN P 304 ASN ** P 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 589 HIS ** P 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 659 GLN ** P 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 861 HIS O 297 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.104721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.092540 restraints weight = 39193.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.094632 restraints weight = 21382.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.096017 restraints weight = 14194.872| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 13885 Z= 0.140 Angle : 0.758 9.106 18898 Z= 0.386 Chirality : 0.046 0.239 2203 Planarity : 0.005 0.067 2478 Dihedral : 6.579 38.249 1909 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.29 % Allowed : 18.03 % Favored : 81.68 % Rotamer: Outliers : 2.56 % Allowed : 14.71 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.94 (0.18), residues: 1714 helix: -2.36 (0.18), residues: 627 sheet: -2.38 (0.36), residues: 188 loop : -4.35 (0.18), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 791 HIS 0.007 0.001 HIS P 752 PHE 0.024 0.002 PHE N 981 TYR 0.024 0.002 TYR N 891 ARG 0.007 0.000 ARG P 777 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 368) hydrogen bonds : angle 5.01259 ( 1020) covalent geometry : bond 0.00323 (13885) covalent geometry : angle 0.75826 (18898) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 880 ARG cc_start: 0.6799 (mmt180) cc_final: 0.6339 (mmt90) REVERT: N 960 LYS cc_start: 0.7116 (mptt) cc_final: 0.6750 (mppt) REVERT: P 241 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7513 (pp) REVERT: P 325 GLN cc_start: 0.8290 (tm-30) cc_final: 0.8060 (tm-30) REVERT: P 408 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8435 (pp) REVERT: P 600 ARG cc_start: 0.7976 (mmp80) cc_final: 0.7756 (mmp80) REVERT: P 637 MET cc_start: 0.8190 (ppp) cc_final: 0.7621 (ppp) REVERT: P 638 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7858 (mtm110) REVERT: P 743 ARG cc_start: 0.8084 (mmm-85) cc_final: 0.7476 (mmm-85) REVERT: P 768 ARG cc_start: 0.8421 (ptp-110) cc_final: 0.7877 (ppt170) REVERT: O 144 GLN cc_start: 0.7935 (mt0) cc_final: 0.7528 (tt0) REVERT: O 268 GLN cc_start: 0.5616 (mt0) cc_final: 0.5082 (mm-40) REVERT: O 309 LYS cc_start: 0.8154 (mttt) cc_final: 0.7879 (mttm) outliers start: 36 outliers final: 19 residues processed: 218 average time/residue: 0.3142 time to fit residues: 94.1959 Evaluate side-chains 205 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain E residue 505 ASN Chi-restraints excluded: chain N residue 980 GLU Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 235 TYR Chi-restraints excluded: chain P residue 237 TYR Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 260 VAL Chi-restraints excluded: chain P residue 270 PHE Chi-restraints excluded: chain P residue 304 ASN Chi-restraints excluded: chain P residue 331 VAL Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 408 LEU Chi-restraints excluded: chain P residue 430 LYS Chi-restraints excluded: chain P residue 482 PHE Chi-restraints excluded: chain P residue 589 HIS Chi-restraints excluded: chain P residue 638 ARG Chi-restraints excluded: chain P residue 644 PHE Chi-restraints excluded: chain P residue 667 PHE Chi-restraints excluded: chain P residue 716 ASP Chi-restraints excluded: chain P residue 928 VAL Chi-restraints excluded: chain O residue 167 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 110 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 55 optimal weight: 0.0670 chunk 88 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 344 GLN P 210 HIS ** P 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 304 ASN ** P 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 297 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.103477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.091099 restraints weight = 39714.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.093193 restraints weight = 21689.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.094568 restraints weight = 14440.185| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13885 Z= 0.170 Angle : 0.765 9.424 18898 Z= 0.390 Chirality : 0.046 0.242 2203 Planarity : 0.006 0.070 2478 Dihedral : 6.602 39.432 1909 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.35 % Allowed : 18.14 % Favored : 81.51 % Rotamer: Outliers : 3.70 % Allowed : 17.20 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.65 (0.19), residues: 1714 helix: -2.03 (0.20), residues: 620 sheet: -2.19 (0.38), residues: 178 loop : -4.23 (0.18), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP P 201 HIS 0.008 0.001 HIS P 752 PHE 0.039 0.002 PHE E 223 TYR 0.025 0.001 TYR N 891 ARG 0.008 0.001 ARG P 182 Details of bonding type rmsd hydrogen bonds : bond 0.03777 ( 368) hydrogen bonds : angle 5.05732 ( 1020) covalent geometry : bond 0.00396 (13885) covalent geometry : angle 0.76549 (18898) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 187 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 869 GLU cc_start: 0.7361 (tm-30) cc_final: 0.7117 (tm-30) REVERT: N 880 ARG cc_start: 0.6785 (mmt180) cc_final: 0.6478 (mmt90) REVERT: P 241 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7484 (pp) REVERT: P 304 ASN cc_start: 0.8620 (OUTLIER) cc_final: 0.8372 (p0) REVERT: P 325 GLN cc_start: 0.8311 (tm-30) cc_final: 0.8035 (tm-30) REVERT: P 408 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8346 (pp) REVERT: P 491 TYR cc_start: 0.6760 (t80) cc_final: 0.5832 (t80) REVERT: P 494 ARG cc_start: 0.7826 (ptt-90) cc_final: 0.7393 (ptt-90) REVERT: P 637 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7529 (ppp) REVERT: P 638 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7984 (mtm110) REVERT: P 768 ARG cc_start: 0.8472 (ptp-110) cc_final: 0.7881 (ppt170) REVERT: O 144 GLN cc_start: 0.8028 (mt0) cc_final: 0.7644 (tt0) REVERT: O 146 GLN cc_start: 0.8454 (tm-30) cc_final: 0.8242 (tm-30) REVERT: O 268 GLN cc_start: 0.5635 (mt0) cc_final: 0.5121 (mm-40) REVERT: O 297 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8256 (pp30) REVERT: O 309 LYS cc_start: 0.8211 (mttt) cc_final: 0.7817 (mttm) outliers start: 52 outliers final: 29 residues processed: 220 average time/residue: 0.2874 time to fit residues: 88.4776 Evaluate side-chains 215 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 505 ASN Chi-restraints excluded: chain N residue 867 VAL Chi-restraints excluded: chain N residue 877 VAL Chi-restraints excluded: chain N residue 980 GLU Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 151 VAL Chi-restraints excluded: chain P residue 192 ILE Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 235 TYR Chi-restraints excluded: chain P residue 237 TYR Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 260 VAL Chi-restraints excluded: chain P residue 270 PHE Chi-restraints excluded: chain P residue 304 ASN Chi-restraints excluded: chain P residue 306 LEU Chi-restraints excluded: chain P residue 331 VAL Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 408 LEU Chi-restraints excluded: chain P residue 430 LYS Chi-restraints excluded: chain P residue 468 VAL Chi-restraints excluded: chain P residue 480 VAL Chi-restraints excluded: chain P residue 482 PHE Chi-restraints excluded: chain P residue 637 MET Chi-restraints excluded: chain P residue 638 ARG Chi-restraints excluded: chain P residue 644 PHE Chi-restraints excluded: chain P residue 667 PHE Chi-restraints excluded: chain P residue 716 ASP Chi-restraints excluded: chain P residue 752 HIS Chi-restraints excluded: chain P residue 790 VAL Chi-restraints excluded: chain P residue 823 THR Chi-restraints excluded: chain P residue 928 VAL Chi-restraints excluded: chain O residue 167 ASN Chi-restraints excluded: chain O residue 267 MET Chi-restraints excluded: chain O residue 297 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 100 optimal weight: 0.4980 chunk 150 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 153 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 96 optimal weight: 0.2980 chunk 86 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 304 ASN ** P 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 589 HIS ** P 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 297 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.104734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.092432 restraints weight = 39263.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.094507 restraints weight = 21705.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.095888 restraints weight = 14542.382| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13885 Z= 0.140 Angle : 0.739 9.207 18898 Z= 0.376 Chirality : 0.045 0.287 2203 Planarity : 0.005 0.072 2478 Dihedral : 6.408 40.300 1909 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.29 % Allowed : 17.39 % Favored : 82.32 % Rotamer: Outliers : 4.41 % Allowed : 18.69 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.37 (0.19), residues: 1714 helix: -1.73 (0.20), residues: 624 sheet: -2.12 (0.38), residues: 185 loop : -4.11 (0.18), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP P 201 HIS 0.007 0.001 HIS P 752 PHE 0.025 0.002 PHE E 223 TYR 0.026 0.001 TYR N 896 ARG 0.007 0.000 ARG P 777 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 368) hydrogen bonds : angle 4.93409 ( 1020) covalent geometry : bond 0.00321 (13885) covalent geometry : angle 0.73884 (18898) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 201 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 869 GLU cc_start: 0.7453 (tm-30) cc_final: 0.7224 (tm-30) REVERT: N 880 ARG cc_start: 0.6742 (mmt180) cc_final: 0.6371 (mmt90) REVERT: P 241 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7365 (pp) REVERT: P 304 ASN cc_start: 0.8496 (OUTLIER) cc_final: 0.8259 (p0) REVERT: P 325 GLN cc_start: 0.8217 (tm-30) cc_final: 0.7945 (tm-30) REVERT: P 408 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8421 (pp) REVERT: P 491 TYR cc_start: 0.6843 (t80) cc_final: 0.6550 (t80) REVERT: P 637 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7504 (ppp) REVERT: P 638 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7915 (mtm110) REVERT: P 743 ARG cc_start: 0.8106 (mmm-85) cc_final: 0.7596 (mmm-85) REVERT: P 768 ARG cc_start: 0.8391 (ptp-110) cc_final: 0.7870 (ppt170) REVERT: O 144 GLN cc_start: 0.7993 (mt0) cc_final: 0.7670 (tt0) REVERT: O 146 GLN cc_start: 0.8404 (tm-30) cc_final: 0.8187 (tm-30) REVERT: O 257 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8216 (tm-30) REVERT: O 268 GLN cc_start: 0.5522 (mt0) cc_final: 0.5073 (mm-40) REVERT: O 309 LYS cc_start: 0.8224 (mttt) cc_final: 0.7805 (mttm) outliers start: 62 outliers final: 35 residues processed: 244 average time/residue: 0.3024 time to fit residues: 105.8473 Evaluate side-chains 227 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 505 ASN Chi-restraints excluded: chain E residue 840 THR Chi-restraints excluded: chain N residue 855 LEU Chi-restraints excluded: chain N residue 867 VAL Chi-restraints excluded: chain N residue 877 VAL Chi-restraints excluded: chain N residue 937 ILE Chi-restraints excluded: chain N residue 965 VAL Chi-restraints excluded: chain N residue 980 GLU Chi-restraints excluded: chain N residue 985 LEU Chi-restraints excluded: chain P residue 151 VAL Chi-restraints excluded: chain P residue 192 ILE Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 235 TYR Chi-restraints excluded: chain P residue 237 TYR Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 270 PHE Chi-restraints excluded: chain P residue 304 ASN Chi-restraints excluded: chain P residue 306 LEU Chi-restraints excluded: chain P residue 331 VAL Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 408 LEU Chi-restraints excluded: chain P residue 430 LYS Chi-restraints excluded: chain P residue 480 VAL Chi-restraints excluded: chain P residue 482 PHE Chi-restraints excluded: chain P residue 637 MET Chi-restraints excluded: chain P residue 638 ARG Chi-restraints excluded: chain P residue 644 PHE Chi-restraints excluded: chain P residue 667 PHE Chi-restraints excluded: chain P residue 716 ASP Chi-restraints excluded: chain P residue 752 HIS Chi-restraints excluded: chain P residue 790 VAL Chi-restraints excluded: chain P residue 823 THR Chi-restraints excluded: chain P residue 928 VAL Chi-restraints excluded: chain O residue 167 ASN Chi-restraints excluded: chain O residue 266 LEU Chi-restraints excluded: chain O residue 285 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 0 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 168 optimal weight: 0.7980 chunk 136 optimal weight: 0.7980 chunk 67 optimal weight: 0.4980 chunk 36 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 154 optimal weight: 0.5980 chunk 126 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 304 ASN ** P 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 589 HIS ** P 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 297 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.104450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.092114 restraints weight = 39293.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.094198 restraints weight = 21617.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.095583 restraints weight = 14449.272| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13885 Z= 0.146 Angle : 0.758 10.337 18898 Z= 0.381 Chirality : 0.046 0.296 2203 Planarity : 0.005 0.071 2478 Dihedral : 6.338 41.174 1909 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.35 % Allowed : 17.44 % Favored : 82.21 % Rotamer: Outliers : 4.41 % Allowed : 20.68 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.20 (0.19), residues: 1714 helix: -1.54 (0.21), residues: 620 sheet: -1.89 (0.40), residues: 171 loop : -4.07 (0.18), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP P 201 HIS 0.008 0.001 HIS P 589 PHE 0.037 0.002 PHE E 223 TYR 0.024 0.001 TYR N 896 ARG 0.010 0.000 ARG P 494 Details of bonding type rmsd hydrogen bonds : bond 0.03392 ( 368) hydrogen bonds : angle 4.92092 ( 1020) covalent geometry : bond 0.00335 (13885) covalent geometry : angle 0.75789 (18898) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 189 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 791 TRP cc_start: 0.7213 (p90) cc_final: 0.6933 (p90) REVERT: N 880 ARG cc_start: 0.6672 (mmt180) cc_final: 0.6350 (mmt90) REVERT: P 241 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7422 (pp) REVERT: P 316 GLN cc_start: 0.6426 (pt0) cc_final: 0.5687 (tm-30) REVERT: P 325 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7935 (tm-30) REVERT: P 408 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8431 (pp) REVERT: P 637 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7421 (ppp) REVERT: P 638 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.8001 (mtm110) REVERT: P 649 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.7081 (tt) REVERT: P 743 ARG cc_start: 0.8039 (mmm-85) cc_final: 0.7606 (mmm-85) REVERT: P 768 ARG cc_start: 0.8381 (ptp-110) cc_final: 0.7861 (ppt170) REVERT: O 144 GLN cc_start: 0.7987 (mt0) cc_final: 0.7688 (tt0) REVERT: O 146 GLN cc_start: 0.8409 (tm-30) cc_final: 0.8188 (tm-30) REVERT: O 257 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8232 (tm-30) REVERT: O 267 MET cc_start: 0.7632 (mtp) cc_final: 0.7184 (mtp) REVERT: O 268 GLN cc_start: 0.5535 (mt0) cc_final: 0.5053 (mm-40) outliers start: 62 outliers final: 43 residues processed: 231 average time/residue: 0.2842 time to fit residues: 92.8234 Evaluate side-chains 233 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 185 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 505 ASN Chi-restraints excluded: chain E residue 840 THR Chi-restraints excluded: chain N residue 824 VAL Chi-restraints excluded: chain N residue 855 LEU Chi-restraints excluded: chain N residue 867 VAL Chi-restraints excluded: chain N residue 877 VAL Chi-restraints excluded: chain N residue 881 LEU Chi-restraints excluded: chain N residue 937 ILE Chi-restraints excluded: chain N residue 965 VAL Chi-restraints excluded: chain N residue 980 GLU Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 151 VAL Chi-restraints excluded: chain P residue 192 ILE Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 235 TYR Chi-restraints excluded: chain P residue 237 TYR Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 260 VAL Chi-restraints excluded: chain P residue 270 PHE Chi-restraints excluded: chain P residue 306 LEU Chi-restraints excluded: chain P residue 331 VAL Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 408 LEU Chi-restraints excluded: chain P residue 480 VAL Chi-restraints excluded: chain P residue 482 PHE Chi-restraints excluded: chain P residue 589 HIS Chi-restraints excluded: chain P residue 624 THR Chi-restraints excluded: chain P residue 637 MET Chi-restraints excluded: chain P residue 638 ARG Chi-restraints excluded: chain P residue 644 PHE Chi-restraints excluded: chain P residue 649 LEU Chi-restraints excluded: chain P residue 667 PHE Chi-restraints excluded: chain P residue 716 ASP Chi-restraints excluded: chain P residue 752 HIS Chi-restraints excluded: chain P residue 780 VAL Chi-restraints excluded: chain P residue 790 VAL Chi-restraints excluded: chain P residue 823 THR Chi-restraints excluded: chain P residue 899 ASN Chi-restraints excluded: chain P residue 908 LEU Chi-restraints excluded: chain P residue 928 VAL Chi-restraints excluded: chain O residue 167 ASN Chi-restraints excluded: chain O residue 266 LEU Chi-restraints excluded: chain O residue 285 ASP Chi-restraints excluded: chain O residue 297 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 74 optimal weight: 0.0470 chunk 18 optimal weight: 2.9990 chunk 71 optimal weight: 0.0020 chunk 154 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 110 optimal weight: 0.7980 chunk 150 optimal weight: 0.4980 chunk 66 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 overall best weight: 0.3686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 210 HIS ** P 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 325 GLN P 589 HIS ** P 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.105859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.093370 restraints weight = 39742.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.095545 restraints weight = 21390.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.096962 restraints weight = 14085.379| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13885 Z= 0.130 Angle : 0.739 9.827 18898 Z= 0.372 Chirality : 0.045 0.273 2203 Planarity : 0.005 0.074 2478 Dihedral : 6.160 41.804 1909 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.23 % Allowed : 17.09 % Favored : 82.67 % Rotamer: Outliers : 4.26 % Allowed : 21.68 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.19), residues: 1714 helix: -1.38 (0.21), residues: 621 sheet: -1.81 (0.39), residues: 172 loop : -3.93 (0.18), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP P 201 HIS 0.018 0.001 HIS P 589 PHE 0.027 0.002 PHE E 223 TYR 0.029 0.001 TYR N 896 ARG 0.009 0.000 ARG P 777 Details of bonding type rmsd hydrogen bonds : bond 0.03065 ( 368) hydrogen bonds : angle 4.78361 ( 1020) covalent geometry : bond 0.00294 (13885) covalent geometry : angle 0.73858 (18898) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 199 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 401 MET cc_start: 0.7703 (tmm) cc_final: 0.7394 (tmm) REVERT: N 880 ARG cc_start: 0.6617 (mmt180) cc_final: 0.6262 (mmt90) REVERT: P 201 TRP cc_start: 0.8010 (p-90) cc_final: 0.7436 (p-90) REVERT: P 241 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7428 (pp) REVERT: P 316 GLN cc_start: 0.6704 (pt0) cc_final: 0.6088 (tm-30) REVERT: P 325 GLN cc_start: 0.8185 (tm130) cc_final: 0.7889 (tm-30) REVERT: P 408 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8364 (pp) REVERT: P 491 TYR cc_start: 0.6626 (t80) cc_final: 0.6392 (t80) REVERT: P 495 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8686 (m-80) REVERT: P 637 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7410 (ppp) REVERT: P 644 PHE cc_start: 0.7038 (OUTLIER) cc_final: 0.6599 (m-10) REVERT: P 649 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6996 (tt) REVERT: P 743 ARG cc_start: 0.8048 (mmm-85) cc_final: 0.7630 (mmm-85) REVERT: P 768 ARG cc_start: 0.8328 (ptp-110) cc_final: 0.7826 (ppt170) REVERT: O 144 GLN cc_start: 0.7945 (mt0) cc_final: 0.7534 (tt0) REVERT: O 146 GLN cc_start: 0.8353 (tm-30) cc_final: 0.8147 (tm-30) REVERT: O 267 MET cc_start: 0.7576 (mtp) cc_final: 0.7056 (mtp) REVERT: O 268 GLN cc_start: 0.5379 (mt0) cc_final: 0.4940 (mm-40) outliers start: 60 outliers final: 41 residues processed: 242 average time/residue: 0.2720 time to fit residues: 92.9311 Evaluate side-chains 235 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 188 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 505 ASN Chi-restraints excluded: chain E residue 840 THR Chi-restraints excluded: chain N residue 828 VAL Chi-restraints excluded: chain N residue 867 VAL Chi-restraints excluded: chain N residue 877 VAL Chi-restraints excluded: chain N residue 881 LEU Chi-restraints excluded: chain N residue 937 ILE Chi-restraints excluded: chain N residue 965 VAL Chi-restraints excluded: chain N residue 980 GLU Chi-restraints excluded: chain N residue 985 LEU Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 151 VAL Chi-restraints excluded: chain P residue 172 PHE Chi-restraints excluded: chain P residue 192 ILE Chi-restraints excluded: chain P residue 235 TYR Chi-restraints excluded: chain P residue 237 TYR Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 260 VAL Chi-restraints excluded: chain P residue 270 PHE Chi-restraints excluded: chain P residue 306 LEU Chi-restraints excluded: chain P residue 331 VAL Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 408 LEU Chi-restraints excluded: chain P residue 480 VAL Chi-restraints excluded: chain P residue 482 PHE Chi-restraints excluded: chain P residue 495 PHE Chi-restraints excluded: chain P residue 589 HIS Chi-restraints excluded: chain P residue 624 THR Chi-restraints excluded: chain P residue 637 MET Chi-restraints excluded: chain P residue 644 PHE Chi-restraints excluded: chain P residue 649 LEU Chi-restraints excluded: chain P residue 667 PHE Chi-restraints excluded: chain P residue 716 ASP Chi-restraints excluded: chain P residue 752 HIS Chi-restraints excluded: chain P residue 780 VAL Chi-restraints excluded: chain P residue 790 VAL Chi-restraints excluded: chain P residue 823 THR Chi-restraints excluded: chain P residue 899 ASN Chi-restraints excluded: chain P residue 908 LEU Chi-restraints excluded: chain P residue 928 VAL Chi-restraints excluded: chain O residue 167 ASN Chi-restraints excluded: chain O residue 266 LEU Chi-restraints excluded: chain O residue 271 LEU Chi-restraints excluded: chain O residue 285 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 137 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 36 optimal weight: 0.1980 chunk 133 optimal weight: 0.6980 chunk 149 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 0.0030 chunk 39 optimal weight: 1.9990 chunk 60 optimal weight: 0.0170 chunk 83 optimal weight: 0.9990 overall best weight: 0.3428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 589 HIS ** P 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 297 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.106563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.094087 restraints weight = 39147.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.096247 restraints weight = 21112.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.097654 restraints weight = 13955.113| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13885 Z= 0.128 Angle : 0.729 9.194 18898 Z= 0.367 Chirality : 0.045 0.279 2203 Planarity : 0.005 0.071 2478 Dihedral : 6.002 42.643 1909 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.29 % Allowed : 16.63 % Favored : 83.08 % Rotamer: Outliers : 3.98 % Allowed : 22.03 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.19), residues: 1714 helix: -1.31 (0.21), residues: 631 sheet: -1.73 (0.39), residues: 170 loop : -3.88 (0.18), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP P 201 HIS 0.023 0.001 HIS P 589 PHE 0.029 0.002 PHE E 223 TYR 0.027 0.001 TYR N 896 ARG 0.011 0.000 ARG P 777 Details of bonding type rmsd hydrogen bonds : bond 0.02928 ( 368) hydrogen bonds : angle 4.68939 ( 1020) covalent geometry : bond 0.00295 (13885) covalent geometry : angle 0.72875 (18898) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 195 time to evaluate : 1.420 Fit side-chains revert: symmetry clash REVERT: E 401 MET cc_start: 0.7899 (tmm) cc_final: 0.7625 (tmm) REVERT: N 880 ARG cc_start: 0.6660 (mmt180) cc_final: 0.6395 (mmt90) REVERT: P 201 TRP cc_start: 0.8022 (p-90) cc_final: 0.7465 (p-90) REVERT: P 241 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7391 (pp) REVERT: P 316 GLN cc_start: 0.6695 (pt0) cc_final: 0.6119 (tm-30) REVERT: P 325 GLN cc_start: 0.8155 (tm130) cc_final: 0.7844 (tm-30) REVERT: P 408 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8433 (pp) REVERT: P 495 PHE cc_start: 0.8988 (OUTLIER) cc_final: 0.8644 (m-80) REVERT: P 637 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7416 (ppp) REVERT: P 644 PHE cc_start: 0.7142 (OUTLIER) cc_final: 0.6670 (m-10) REVERT: P 649 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6969 (tt) REVERT: P 768 ARG cc_start: 0.8291 (ptp-110) cc_final: 0.7808 (ppt170) REVERT: O 264 ARG cc_start: 0.7366 (mtt180) cc_final: 0.6771 (ttm170) REVERT: O 267 MET cc_start: 0.7487 (mtp) cc_final: 0.6952 (mtp) REVERT: O 268 GLN cc_start: 0.5329 (mt0) cc_final: 0.4901 (mm-40) outliers start: 56 outliers final: 43 residues processed: 231 average time/residue: 0.2842 time to fit residues: 92.4223 Evaluate side-chains 232 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 183 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 505 ASN Chi-restraints excluded: chain E residue 840 THR Chi-restraints excluded: chain N residue 828 VAL Chi-restraints excluded: chain N residue 855 LEU Chi-restraints excluded: chain N residue 877 VAL Chi-restraints excluded: chain N residue 881 LEU Chi-restraints excluded: chain N residue 937 ILE Chi-restraints excluded: chain N residue 965 VAL Chi-restraints excluded: chain N residue 980 GLU Chi-restraints excluded: chain N residue 985 LEU Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 151 VAL Chi-restraints excluded: chain P residue 172 PHE Chi-restraints excluded: chain P residue 192 ILE Chi-restraints excluded: chain P residue 235 TYR Chi-restraints excluded: chain P residue 237 TYR Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 260 VAL Chi-restraints excluded: chain P residue 270 PHE Chi-restraints excluded: chain P residue 306 LEU Chi-restraints excluded: chain P residue 315 LYS Chi-restraints excluded: chain P residue 331 VAL Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 408 LEU Chi-restraints excluded: chain P residue 480 VAL Chi-restraints excluded: chain P residue 482 PHE Chi-restraints excluded: chain P residue 495 PHE Chi-restraints excluded: chain P residue 624 THR Chi-restraints excluded: chain P residue 637 MET Chi-restraints excluded: chain P residue 644 PHE Chi-restraints excluded: chain P residue 649 LEU Chi-restraints excluded: chain P residue 667 PHE Chi-restraints excluded: chain P residue 716 ASP Chi-restraints excluded: chain P residue 752 HIS Chi-restraints excluded: chain P residue 780 VAL Chi-restraints excluded: chain P residue 790 VAL Chi-restraints excluded: chain P residue 823 THR Chi-restraints excluded: chain P residue 899 ASN Chi-restraints excluded: chain P residue 908 LEU Chi-restraints excluded: chain P residue 928 VAL Chi-restraints excluded: chain O residue 167 ASN Chi-restraints excluded: chain O residue 266 LEU Chi-restraints excluded: chain O residue 271 LEU Chi-restraints excluded: chain O residue 285 ASP Chi-restraints excluded: chain O residue 297 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 147 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 115 optimal weight: 0.5980 chunk 146 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 29 optimal weight: 0.0030 chunk 63 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 210 HIS ** P 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 149 GLN O 297 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.106012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.093642 restraints weight = 39294.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.095762 restraints weight = 21389.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.097173 restraints weight = 14202.988| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 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 0.050 13885 Z= 0.135 Angle : 0.734 9.883 18898 Z= 0.370 Chirality : 0.045 0.296 2203 Planarity : 0.005 0.071 2478 Dihedral : 5.979 43.220 1909 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.29 % Allowed : 16.92 % Favored : 82.79 % Rotamer: Outliers : 4.12 % Allowed : 22.74 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.20), residues: 1714 helix: -1.25 (0.21), residues: 632 sheet: -1.65 (0.40), residues: 170 loop : -3.83 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 245 HIS 0.006 0.001 HIS P 752 PHE 0.025 0.002 PHE E 223 TYR 0.034 0.001 TYR P 491 ARG 0.007 0.000 ARG P 743 Details of bonding type rmsd hydrogen bonds : bond 0.03053 ( 368) hydrogen bonds : angle 4.67444 ( 1020) covalent geometry : bond 0.00313 (13885) covalent geometry : angle 0.73412 (18898) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 190 time to evaluate : 1.462 Fit side-chains revert: symmetry clash REVERT: E 401 MET cc_start: 0.7920 (tmm) cc_final: 0.7651 (tmm) REVERT: E 685 ASP cc_start: 0.7273 (t0) cc_final: 0.6990 (t70) REVERT: N 869 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7294 (tm-30) REVERT: N 880 ARG cc_start: 0.6681 (mmt180) cc_final: 0.6366 (mmt90) REVERT: P 201 TRP cc_start: 0.8005 (p-90) cc_final: 0.7380 (p-90) REVERT: P 241 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7400 (pp) REVERT: P 316 GLN cc_start: 0.6859 (pt0) cc_final: 0.6211 (tm-30) REVERT: P 325 GLN cc_start: 0.8172 (tm130) cc_final: 0.7925 (tm-30) REVERT: P 408 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8425 (pp) REVERT: P 495 PHE cc_start: 0.8962 (OUTLIER) cc_final: 0.8626 (m-80) REVERT: P 637 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7451 (ppp) REVERT: P 644 PHE cc_start: 0.7056 (OUTLIER) cc_final: 0.6632 (m-10) REVERT: P 649 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.7010 (tt) REVERT: P 768 ARG cc_start: 0.8289 (ptp-110) cc_final: 0.7819 (ppt170) REVERT: O 264 ARG cc_start: 0.7358 (mtt180) cc_final: 0.6734 (ttm170) REVERT: O 267 MET cc_start: 0.7497 (mtp) cc_final: 0.6961 (mtp) REVERT: O 268 GLN cc_start: 0.5246 (mt0) cc_final: 0.4798 (mm-40) outliers start: 58 outliers final: 45 residues processed: 229 average time/residue: 0.2937 time to fit residues: 94.4254 Evaluate side-chains 235 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 184 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 505 ASN Chi-restraints excluded: chain E residue 840 THR Chi-restraints excluded: chain N residue 828 VAL Chi-restraints excluded: chain N residue 855 LEU Chi-restraints excluded: chain N residue 867 VAL Chi-restraints excluded: chain N residue 877 VAL Chi-restraints excluded: chain N residue 881 LEU Chi-restraints excluded: chain N residue 937 ILE Chi-restraints excluded: chain N residue 965 VAL Chi-restraints excluded: chain N residue 975 LEU Chi-restraints excluded: chain N residue 980 GLU Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 151 VAL Chi-restraints excluded: chain P residue 192 ILE Chi-restraints excluded: chain P residue 235 TYR Chi-restraints excluded: chain P residue 237 TYR Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 260 VAL Chi-restraints excluded: chain P residue 270 PHE Chi-restraints excluded: chain P residue 306 LEU Chi-restraints excluded: chain P residue 315 LYS Chi-restraints excluded: chain P residue 331 VAL Chi-restraints excluded: chain P residue 408 LEU Chi-restraints excluded: chain P residue 480 VAL Chi-restraints excluded: chain P residue 482 PHE Chi-restraints excluded: chain P residue 495 PHE Chi-restraints excluded: chain P residue 624 THR Chi-restraints excluded: chain P residue 637 MET Chi-restraints excluded: chain P residue 644 PHE Chi-restraints excluded: chain P residue 649 LEU Chi-restraints excluded: chain P residue 667 PHE Chi-restraints excluded: chain P residue 716 ASP Chi-restraints excluded: chain P residue 737 MET Chi-restraints excluded: chain P residue 752 HIS Chi-restraints excluded: chain P residue 780 VAL Chi-restraints excluded: chain P residue 790 VAL Chi-restraints excluded: chain P residue 823 THR Chi-restraints excluded: chain P residue 899 ASN Chi-restraints excluded: chain P residue 908 LEU Chi-restraints excluded: chain P residue 928 VAL Chi-restraints excluded: chain P residue 942 GLU Chi-restraints excluded: chain P residue 947 LEU Chi-restraints excluded: chain O residue 167 ASN Chi-restraints excluded: chain O residue 266 LEU Chi-restraints excluded: chain O residue 271 LEU Chi-restraints excluded: chain O residue 285 ASP Chi-restraints excluded: chain O residue 297 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 118 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 160 optimal weight: 0.1980 chunk 23 optimal weight: 0.4980 chunk 123 optimal weight: 0.9990 chunk 45 optimal weight: 0.0980 chunk 37 optimal weight: 0.6980 chunk 168 optimal weight: 0.9980 chunk 144 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 752 HIS ** P 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 297 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.106623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.094317 restraints weight = 38695.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.096421 restraints weight = 21265.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.097815 restraints weight = 14206.547| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13885 Z= 0.128 Angle : 0.730 9.646 18898 Z= 0.367 Chirality : 0.045 0.286 2203 Planarity : 0.005 0.070 2478 Dihedral : 5.904 43.664 1909 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.29 % Allowed : 16.92 % Favored : 82.79 % Rotamer: Outliers : 4.05 % Allowed : 23.10 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.20), residues: 1714 helix: -1.20 (0.21), residues: 635 sheet: -1.61 (0.40), residues: 170 loop : -3.76 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP P 245 HIS 0.006 0.001 HIS P 752 PHE 0.038 0.002 PHE E 223 TYR 0.026 0.001 TYR N 896 ARG 0.010 0.000 ARG P 777 Details of bonding type rmsd hydrogen bonds : bond 0.02893 ( 368) hydrogen bonds : angle 4.64770 ( 1020) covalent geometry : bond 0.00297 (13885) covalent geometry : angle 0.73048 (18898) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 191 time to evaluate : 1.600 Fit side-chains revert: symmetry clash REVERT: E 401 MET cc_start: 0.7881 (tmm) cc_final: 0.7621 (tmm) REVERT: E 474 PRO cc_start: 0.7115 (Cg_exo) cc_final: 0.6852 (Cg_endo) REVERT: N 869 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7360 (tm-30) REVERT: N 880 ARG cc_start: 0.6590 (mmt180) cc_final: 0.6261 (mmt90) REVERT: P 201 TRP cc_start: 0.7958 (p-90) cc_final: 0.7599 (p-90) REVERT: P 241 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7416 (pp) REVERT: P 316 GLN cc_start: 0.6888 (pt0) cc_final: 0.6264 (tm-30) REVERT: P 408 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8424 (pp) REVERT: P 409 TYR cc_start: 0.6135 (p90) cc_final: 0.4703 (p90) REVERT: P 495 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8583 (m-80) REVERT: P 637 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7464 (ppp) REVERT: P 644 PHE cc_start: 0.7142 (OUTLIER) cc_final: 0.6675 (m-10) REVERT: P 649 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6997 (tt) REVERT: P 768 ARG cc_start: 0.8254 (ptp-110) cc_final: 0.7788 (ppt170) REVERT: O 264 ARG cc_start: 0.7330 (mtt180) cc_final: 0.6756 (ttm170) REVERT: O 267 MET cc_start: 0.7493 (mtp) cc_final: 0.7249 (mtp) REVERT: O 268 GLN cc_start: 0.5235 (mt0) cc_final: 0.4819 (mm-40) outliers start: 57 outliers final: 47 residues processed: 229 average time/residue: 0.2887 time to fit residues: 93.5267 Evaluate side-chains 236 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 183 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 488 LEU Chi-restraints excluded: chain E residue 505 ASN Chi-restraints excluded: chain E residue 840 THR Chi-restraints excluded: chain N residue 828 VAL Chi-restraints excluded: chain N residue 855 LEU Chi-restraints excluded: chain N residue 867 VAL Chi-restraints excluded: chain N residue 877 VAL Chi-restraints excluded: chain N residue 881 LEU Chi-restraints excluded: chain N residue 937 ILE Chi-restraints excluded: chain N residue 965 VAL Chi-restraints excluded: chain N residue 975 LEU Chi-restraints excluded: chain N residue 980 GLU Chi-restraints excluded: chain N residue 985 LEU Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 172 PHE Chi-restraints excluded: chain P residue 192 ILE Chi-restraints excluded: chain P residue 235 TYR Chi-restraints excluded: chain P residue 237 TYR Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 260 VAL Chi-restraints excluded: chain P residue 306 LEU Chi-restraints excluded: chain P residue 315 LYS Chi-restraints excluded: chain P residue 331 VAL Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 408 LEU Chi-restraints excluded: chain P residue 480 VAL Chi-restraints excluded: chain P residue 482 PHE Chi-restraints excluded: chain P residue 495 PHE Chi-restraints excluded: chain P residue 574 LEU Chi-restraints excluded: chain P residue 624 THR Chi-restraints excluded: chain P residue 637 MET Chi-restraints excluded: chain P residue 644 PHE Chi-restraints excluded: chain P residue 649 LEU Chi-restraints excluded: chain P residue 716 ASP Chi-restraints excluded: chain P residue 737 MET Chi-restraints excluded: chain P residue 752 HIS Chi-restraints excluded: chain P residue 779 GLN Chi-restraints excluded: chain P residue 780 VAL Chi-restraints excluded: chain P residue 790 VAL Chi-restraints excluded: chain P residue 823 THR Chi-restraints excluded: chain P residue 899 ASN Chi-restraints excluded: chain P residue 908 LEU Chi-restraints excluded: chain P residue 928 VAL Chi-restraints excluded: chain P residue 942 GLU Chi-restraints excluded: chain P residue 947 LEU Chi-restraints excluded: chain O residue 266 LEU Chi-restraints excluded: chain O residue 271 LEU Chi-restraints excluded: chain O residue 285 ASP Chi-restraints excluded: chain O residue 297 GLN Chi-restraints excluded: chain O residue 303 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 9 optimal weight: 0.0570 chunk 158 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 73 optimal weight: 0.4980 chunk 177 optimal weight: 4.9990 chunk 156 optimal weight: 0.7980 chunk 166 optimal weight: 0.0270 chunk 48 optimal weight: 0.6980 chunk 165 optimal weight: 0.0770 chunk 43 optimal weight: 0.8980 overall best weight: 0.2714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 210 HIS P 232 GLN ** P 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 297 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.107536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.095246 restraints weight = 39055.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.097351 restraints weight = 21297.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.098746 restraints weight = 14182.134| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13885 Z= 0.126 Angle : 0.735 9.774 18898 Z= 0.369 Chirality : 0.044 0.292 2203 Planarity : 0.005 0.070 2478 Dihedral : 5.803 43.981 1909 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.23 % Allowed : 16.22 % Favored : 83.55 % Rotamer: Outliers : 3.91 % Allowed : 23.24 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.20), residues: 1714 helix: -1.13 (0.21), residues: 637 sheet: -1.41 (0.42), residues: 155 loop : -3.61 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP P 245 HIS 0.005 0.001 HIS P 752 PHE 0.024 0.001 PHE E 223 TYR 0.036 0.001 TYR P 491 ARG 0.012 0.000 ARG P 777 Details of bonding type rmsd hydrogen bonds : bond 0.02765 ( 368) hydrogen bonds : angle 4.55677 ( 1020) covalent geometry : bond 0.00291 (13885) covalent geometry : angle 0.73541 (18898) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3428 Ramachandran restraints generated. 1714 Oldfield, 0 Emsley, 1714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 194 time to evaluate : 1.532 Fit side-chains revert: symmetry clash REVERT: E 362 LEU cc_start: 0.7722 (mp) cc_final: 0.7489 (pp) REVERT: E 401 MET cc_start: 0.7849 (tmm) cc_final: 0.7618 (tmm) REVERT: E 474 PRO cc_start: 0.6985 (Cg_exo) cc_final: 0.6742 (Cg_endo) REVERT: E 685 ASP cc_start: 0.7134 (t0) cc_final: 0.6832 (t70) REVERT: N 869 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7363 (tm-30) REVERT: N 880 ARG cc_start: 0.6433 (mmt180) cc_final: 0.6157 (mmt90) REVERT: P 201 TRP cc_start: 0.7952 (p-90) cc_final: 0.7583 (p-90) REVERT: P 232 GLN cc_start: 0.6771 (OUTLIER) cc_final: 0.6264 (mm-40) REVERT: P 241 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7348 (pp) REVERT: P 316 GLN cc_start: 0.6935 (pt0) cc_final: 0.6416 (tm-30) REVERT: P 408 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8424 (pp) REVERT: P 495 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.8494 (m-80) REVERT: P 504 GLN cc_start: 0.8302 (pp30) cc_final: 0.7954 (pt0) REVERT: P 637 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7484 (ppp) REVERT: P 644 PHE cc_start: 0.7144 (OUTLIER) cc_final: 0.6671 (m-10) REVERT: P 649 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6933 (tt) REVERT: P 768 ARG cc_start: 0.8234 (ptp-110) cc_final: 0.7798 (ppt170) REVERT: O 267 MET cc_start: 0.7478 (mtp) cc_final: 0.7244 (mtp) REVERT: O 268 GLN cc_start: 0.5281 (mt0) cc_final: 0.4834 (mm-40) outliers start: 55 outliers final: 43 residues processed: 229 average time/residue: 0.2879 time to fit residues: 93.4532 Evaluate side-chains 239 residues out of total 1503 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 189 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 404 PHE Chi-restraints excluded: chain E residue 447 PHE Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 505 ASN Chi-restraints excluded: chain E residue 840 THR Chi-restraints excluded: chain N residue 828 VAL Chi-restraints excluded: chain N residue 855 LEU Chi-restraints excluded: chain N residue 877 VAL Chi-restraints excluded: chain N residue 881 LEU Chi-restraints excluded: chain N residue 965 VAL Chi-restraints excluded: chain N residue 975 LEU Chi-restraints excluded: chain N residue 980 GLU Chi-restraints excluded: chain N residue 985 LEU Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 172 PHE Chi-restraints excluded: chain P residue 192 ILE Chi-restraints excluded: chain P residue 232 GLN Chi-restraints excluded: chain P residue 235 TYR Chi-restraints excluded: chain P residue 237 TYR Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 260 VAL Chi-restraints excluded: chain P residue 306 LEU Chi-restraints excluded: chain P residue 315 LYS Chi-restraints excluded: chain P residue 331 VAL Chi-restraints excluded: chain P residue 355 THR Chi-restraints excluded: chain P residue 408 LEU Chi-restraints excluded: chain P residue 480 VAL Chi-restraints excluded: chain P residue 482 PHE Chi-restraints excluded: chain P residue 495 PHE Chi-restraints excluded: chain P residue 574 LEU Chi-restraints excluded: chain P residue 624 THR Chi-restraints excluded: chain P residue 637 MET Chi-restraints excluded: chain P residue 644 PHE Chi-restraints excluded: chain P residue 649 LEU Chi-restraints excluded: chain P residue 667 PHE Chi-restraints excluded: chain P residue 716 ASP Chi-restraints excluded: chain P residue 737 MET Chi-restraints excluded: chain P residue 752 HIS Chi-restraints excluded: chain P residue 780 VAL Chi-restraints excluded: chain P residue 790 VAL Chi-restraints excluded: chain P residue 823 THR Chi-restraints excluded: chain P residue 899 ASN Chi-restraints excluded: chain P residue 908 LEU Chi-restraints excluded: chain P residue 928 VAL Chi-restraints excluded: chain P residue 942 GLU Chi-restraints excluded: chain O residue 266 LEU Chi-restraints excluded: chain O residue 271 LEU Chi-restraints excluded: chain O residue 285 ASP Chi-restraints excluded: chain O residue 297 GLN Chi-restraints excluded: chain O residue 303 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 71 optimal weight: 0.2980 chunk 145 optimal weight: 0.8980 chunk 174 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 155 optimal weight: 0.0270 chunk 92 optimal weight: 0.9990 chunk 146 optimal weight: 0.2980 chunk 126 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 210 HIS ** P 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 297 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 = 0.3721 r_free = 0.3721 target = 0.107296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.094937 restraints weight = 39287.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.097082 restraints weight = 21399.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.098518 restraints weight = 14173.626| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 13885 Z= 0.224 Angle : 0.957 59.174 18898 Z= 0.527 Chirality : 0.045 0.241 2203 Planarity : 0.006 0.146 2478 Dihedral : 5.812 44.034 1909 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.23 % Allowed : 16.28 % Favored : 83.49 % Rotamer: Outliers : 3.84 % Allowed : 23.45 % Favored : 72.71 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.20), residues: 1714 helix: -1.12 (0.21), residues: 637 sheet: -1.37 (0.42), residues: 155 loop : -3.61 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 245 HIS 0.027 0.001 HIS P 760 PHE 0.023 0.001 PHE E 223 TYR 0.048 0.002 TYR P 501 ARG 0.011 0.001 ARG P 777 Details of bonding type rmsd hydrogen bonds : bond 0.02835 ( 368) hydrogen bonds : angle 4.55688 ( 1020) covalent geometry : bond 0.00394 (13885) covalent geometry : angle 0.95745 (18898) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4877.69 seconds wall clock time: 84 minutes 49.80 seconds (5089.80 seconds total)