Starting phenix.real_space_refine on Fri Mar 6 04:28:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tet_25852/03_2026/7tet_25852.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tet_25852/03_2026/7tet_25852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tet_25852/03_2026/7tet_25852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tet_25852/03_2026/7tet_25852.map" model { file = "/net/cci-nas-00/data/ceres_data/7tet_25852/03_2026/7tet_25852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tet_25852/03_2026/7tet_25852.cif" } resolution = 4.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.044 sd= 0.420 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 172 5.16 5 C 17941 2.51 5 N 4707 2.21 5 O 5268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28088 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 6194 Classifications: {'peptide': 786} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 753} Chain breaks: 5 Chain: "B" Number of atoms: 6079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 769, 6079 Classifications: {'peptide': 769} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 26, 'TRANS': 740} Chain breaks: 5 Chain: "C" Number of atoms: 6194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 6194 Classifications: {'peptide': 786} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 753} Chain breaks: 5 Chain: "D" Number of atoms: 6085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 770, 6085 Classifications: {'peptide': 770} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 26, 'TRANS': 741} Chain breaks: 4 Chain: "H" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 893 Classifications: {'peptide': 114} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 110} Chain: "L" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 875 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "M" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 893 Classifications: {'peptide': 114} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 110} Chain: "N" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 875 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Time building chain proxies: 5.99, per 1000 atoms: 0.21 Number of scatterers: 28088 At special positions: 0 Unit cell: (141.11, 205.5, 182.21, 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 172 16.00 O 5268 8.00 N 4707 7.00 C 17941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.03 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.04 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 329 " distance=2.03 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 476 " distance=2.03 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.03 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.04 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 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: 2.02 Conformation dependent library (CDL) restraints added in 1.1 seconds 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6626 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 46 sheets defined 38.1% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 35 through 49 removed outlier: 3.500A pdb=" N GLU A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 52 No H-bonds generated for 'chain 'A' and resid 50 through 52' Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.887A pdb=" N TYR A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N THR A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 170 through 185 removed outlier: 3.623A pdb=" N GLU A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 245 through 259 Processing helix chain 'A' and resid 276 through 283 removed outlier: 3.716A pdb=" N TYR A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 317 removed outlier: 3.507A pdb=" N HIS A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 349 removed outlier: 4.357A pdb=" N LEU A 341 " --> pdb=" O LYS A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 491 removed outlier: 3.926A pdb=" N ASP A 482 " --> pdb=" O GLY A 478 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 483 " --> pdb=" O PHE A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 528 Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 582 through 602 removed outlier: 3.981A pdb=" N LEU A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 637 removed outlier: 4.076A pdb=" N PHE A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER A 631 " --> pdb=" O ALA A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 677 removed outlier: 3.715A pdb=" N ARG A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 695 Processing helix chain 'A' and resid 708 through 717 Processing helix chain 'A' and resid 720 through 729 removed outlier: 3.980A pdb=" N LYS A 729 " --> pdb=" O ARG A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 745 removed outlier: 3.929A pdb=" N ALA A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG A 743 " --> pdb=" O ILE A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 764 removed outlier: 4.077A pdb=" N PHE A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 802 Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 832 through 842 removed outlier: 3.735A pdb=" N ALA A 835 " --> pdb=" O GLU A 832 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY A 836 " --> pdb=" O ASN A 833 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N MET A 839 " --> pdb=" O GLY A 836 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 840 " --> pdb=" O VAL A 837 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 841 " --> pdb=" O PHE A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 862 Processing helix chain 'B' and resid 46 through 54 removed outlier: 4.393A pdb=" N HIS B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 removed outlier: 3.725A pdb=" N HIS B 60 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 removed outlier: 3.541A pdb=" N ILE B 85 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 93 removed outlier: 3.744A pdb=" N ARG B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 119 Processing helix chain 'B' and resid 149 through 164 removed outlier: 3.528A pdb=" N GLN B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 192 removed outlier: 4.766A pdb=" N PHE B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B 183 " --> pdb=" O TYR B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 222 removed outlier: 3.846A pdb=" N LYS B 222 " --> pdb=" O ASN B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 259 through 264 Processing helix chain 'B' and resid 282 through 308 removed outlier: 3.831A pdb=" N ASP B 286 " --> pdb=" O TYR B 282 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU B 289 " --> pdb=" O TRP B 285 " (cutoff:3.500A) Proline residue: B 290 - end of helix removed outlier: 3.521A pdb=" N ALA B 298 " --> pdb=" O ARG B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 331 removed outlier: 3.687A pdb=" N GLN B 331 " --> pdb=" O ARG B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 459 through 472 removed outlier: 4.168A pdb=" N ASP B 463 " --> pdb=" O GLY B 459 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE B 464 " --> pdb=" O PHE B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 503 removed outlier: 3.609A pdb=" N MET B 503 " --> pdb=" O GLY B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 519 No H-bonds generated for 'chain 'B' and resid 518 through 519' Processing helix chain 'B' and resid 521 through 523 No H-bonds generated for 'chain 'B' and resid 521 through 523' Processing helix chain 'B' and resid 551 through 576 removed outlier: 3.709A pdb=" N CYS B 557 " --> pdb=" O PRO B 553 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL B 558 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N MET B 561 " --> pdb=" O CYS B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 608 removed outlier: 3.531A pdb=" N TRP B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 614 Processing helix chain 'B' and resid 626 through 655 removed outlier: 3.640A pdb=" N ILE B 630 " --> pdb=" O THR B 626 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE B 638 " --> pdb=" O VAL B 634 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 655 " --> pdb=" O ALA B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 673 removed outlier: 4.082A pdb=" N ASP B 668 " --> pdb=" O SER B 664 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N PHE B 671 " --> pdb=" O SER B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 699 removed outlier: 3.874A pdb=" N ARG B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 704 Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.932A pdb=" N ASN B 710 " --> pdb=" O GLY B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 723 removed outlier: 3.519A pdb=" N ALA B 717 " --> pdb=" O GLY B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 Processing helix chain 'B' and resid 771 through 785 removed outlier: 3.662A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 778 " --> pdb=" O ARG B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.514A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 821 removed outlier: 3.825A pdb=" N ALA B 819 " --> pdb=" O ASP B 816 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY B 820 " --> pdb=" O ASN B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 824 through 843 Processing helix chain 'C' and resid 35 through 49 removed outlier: 3.500A pdb=" N GLU C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 52 No H-bonds generated for 'chain 'C' and resid 50 through 52' Processing helix chain 'C' and resid 70 through 75 Processing helix chain 'C' and resid 104 through 114 removed outlier: 3.886A pdb=" N TYR C 109 " --> pdb=" O THR C 105 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N THR C 110 " --> pdb=" O PRO C 106 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA C 111 " --> pdb=" O VAL C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 146 No H-bonds generated for 'chain 'C' and resid 144 through 146' Processing helix chain 'C' and resid 147 through 153 Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 170 through 185 removed outlier: 3.622A pdb=" N GLU C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 231 through 234 Processing helix chain 'C' and resid 245 through 259 Processing helix chain 'C' and resid 276 through 283 removed outlier: 3.716A pdb=" N TYR C 282 " --> pdb=" O ASN C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 317 removed outlier: 3.507A pdb=" N HIS C 301 " --> pdb=" O ASN C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 349 removed outlier: 4.356A pdb=" N LEU C 341 " --> pdb=" O LYS C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 491 removed outlier: 3.926A pdb=" N ASP C 482 " --> pdb=" O GLY C 478 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU C 483 " --> pdb=" O PHE C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 528 Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 582 through 602 removed outlier: 3.980A pdb=" N LEU C 589 " --> pdb=" O LEU C 585 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS C 592 " --> pdb=" O GLY C 588 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET C 597 " --> pdb=" O VAL C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 637 removed outlier: 4.075A pdb=" N PHE C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER C 631 " --> pdb=" O ALA C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 677 removed outlier: 3.716A pdb=" N ARG C 651 " --> pdb=" O SER C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 695 Processing helix chain 'C' and resid 708 through 717 Processing helix chain 'C' and resid 720 through 729 removed outlier: 3.980A pdb=" N LYS C 729 " --> pdb=" O ARG C 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 745 removed outlier: 3.928A pdb=" N ALA C 738 " --> pdb=" O SER C 734 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG C 743 " --> pdb=" O ILE C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 764 removed outlier: 4.078A pdb=" N PHE C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 802 Processing helix chain 'C' and resid 804 through 814 Processing helix chain 'C' and resid 832 through 842 removed outlier: 3.736A pdb=" N ALA C 835 " --> pdb=" O GLU C 832 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY C 836 " --> pdb=" O ASN C 833 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N MET C 839 " --> pdb=" O GLY C 836 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU C 840 " --> pdb=" O VAL C 837 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL C 841 " --> pdb=" O PHE C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 862 Processing helix chain 'D' and resid 46 through 54 removed outlier: 4.407A pdb=" N HIS D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 removed outlier: 3.722A pdb=" N HIS D 60 " --> pdb=" O ASP D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 88 removed outlier: 3.514A pdb=" N ILE D 85 " --> pdb=" O ILE D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 93 removed outlier: 3.723A pdb=" N ARG D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 119 Processing helix chain 'D' and resid 149 through 164 removed outlier: 3.563A pdb=" N GLN D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 192 removed outlier: 4.715A pdb=" N PHE D 182 " --> pdb=" O GLY D 178 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL D 183 " --> pdb=" O TYR D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 222 removed outlier: 3.832A pdb=" N LYS D 222 " --> pdb=" O ASN D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 259 through 264 Processing helix chain 'D' and resid 282 through 308 removed outlier: 3.881A pdb=" N ASP D 286 " --> pdb=" O TYR D 282 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU D 289 " --> pdb=" O TRP D 285 " (cutoff:3.500A) Proline residue: D 290 - end of helix removed outlier: 3.500A pdb=" N ALA D 298 " --> pdb=" O ARG D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 331 removed outlier: 3.702A pdb=" N GLN D 331 " --> pdb=" O ARG D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 459 through 472 removed outlier: 4.150A pdb=" N ASP D 463 " --> pdb=" O GLY D 459 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE D 464 " --> pdb=" O PHE D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 503 Processing helix chain 'D' and resid 516 through 523 removed outlier: 3.602A pdb=" N GLU D 521 " --> pdb=" O GLU D 517 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL D 522 " --> pdb=" O GLU D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 576 removed outlier: 4.223A pdb=" N MET D 561 " --> pdb=" O CYS D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 608 removed outlier: 3.558A pdb=" N TRP D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 614 Processing helix chain 'D' and resid 626 through 655 removed outlier: 3.638A pdb=" N ILE D 630 " --> pdb=" O THR D 626 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE D 638 " --> pdb=" O VAL D 634 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE D 655 " --> pdb=" O ALA D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 667 removed outlier: 3.609A pdb=" N LEU D 666 " --> pdb=" O GLN D 662 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 689 through 699 removed outlier: 4.177A pdb=" N ARG D 693 " --> pdb=" O GLY D 689 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN D 694 " --> pdb=" O SER D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 704 Processing helix chain 'D' and resid 706 through 710 removed outlier: 3.936A pdb=" N ASN D 710 " --> pdb=" O GLY D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 723 removed outlier: 3.520A pdb=" N ALA D 717 " --> pdb=" O GLY D 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 771 through 785 removed outlier: 3.713A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 778 " --> pdb=" O ARG D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 797 removed outlier: 3.512A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 821 removed outlier: 3.800A pdb=" N ALA D 819 " --> pdb=" O ASP D 816 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY D 820 " --> pdb=" O ASN D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 824 through 844 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.628A pdb=" N ASP H 90 " --> pdb=" O LYS H 87 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'M' and resid 87 through 91 removed outlier: 3.627A pdb=" N ASP M 90 " --> pdb=" O LYS M 87 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR M 91 " --> pdb=" O SER M 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 62 removed outlier: 5.964A pdb=" N VAL A 27 " --> pdb=" O GLN A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 62 removed outlier: 5.964A pdb=" N VAL A 27 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL A 87 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASN A 28 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ALA A 89 " --> pdb=" O ASN A 28 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 216 through 218 removed outlier: 3.632A pdb=" N SER A 243 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE A 240 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 288 through 292 removed outlier: 6.306A pdb=" N TYR A 372 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE A 387 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE A 374 " --> pdb=" O VAL A 385 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 420 through 423 removed outlier: 3.514A pdb=" N HIS A 498 " --> pdb=" O ILE A 421 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 508 through 511 removed outlier: 3.910A pdb=" N LYS A 516 " --> pdb=" O VAL A 511 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 533 through 535 Processing sheet with id=AA8, first strand: chain 'A' and resid 750 through 753 Processing sheet with id=AA9, first strand: chain 'A' and resid 750 through 753 Processing sheet with id=AB1, first strand: chain 'B' and resid 66 through 73 removed outlier: 6.143A pdb=" N GLY B 36 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL B 98 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ALA B 38 " --> pdb=" O VAL B 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 201 through 204 removed outlier: 3.640A pdb=" N SER B 170 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE B 228 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 278 through 280 Processing sheet with id=AB4, first strand: chain 'B' and resid 341 through 344 removed outlier: 3.910A pdb=" N VAL B 342 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 377 through 379 Processing sheet with id=AB6, first strand: chain 'B' and resid 475 through 480 Processing sheet with id=AB7, first strand: chain 'B' and resid 418 through 420 Processing sheet with id=AB8, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AB9, first strand: chain 'B' and resid 530 through 532 removed outlier: 4.125A pdb=" N ILE B 530 " --> pdb=" O TYR B 762 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 534 through 537 Processing sheet with id=AC2, first strand: chain 'C' and resid 59 through 62 removed outlier: 5.964A pdb=" N VAL C 27 " --> pdb=" O GLN C 61 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 59 through 62 removed outlier: 5.964A pdb=" N VAL C 27 " --> pdb=" O GLN C 61 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL C 87 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN C 28 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ALA C 89 " --> pdb=" O ASN C 28 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 216 through 218 removed outlier: 3.631A pdb=" N SER C 243 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE C 240 " --> pdb=" O LEU C 269 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 288 through 292 removed outlier: 6.307A pdb=" N TYR C 372 " --> pdb=" O ILE C 387 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE C 387 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE C 374 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 420 through 423 removed outlier: 3.513A pdb=" N HIS C 498 " --> pdb=" O ILE C 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 508 through 511 removed outlier: 3.909A pdb=" N LYS C 516 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 533 through 535 Processing sheet with id=AC9, first strand: chain 'C' and resid 750 through 753 Processing sheet with id=AD1, first strand: chain 'C' and resid 750 through 753 Processing sheet with id=AD2, first strand: chain 'D' and resid 66 through 73 removed outlier: 6.167A pdb=" N GLY D 36 " --> pdb=" O GLY D 96 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL D 98 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ALA D 38 " --> pdb=" O VAL D 98 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 201 through 204 removed outlier: 3.643A pdb=" N SER D 170 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE D 228 " --> pdb=" O ILE D 257 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 278 through 280 Processing sheet with id=AD5, first strand: chain 'D' and resid 341 through 344 removed outlier: 3.871A pdb=" N VAL D 342 " --> pdb=" O LEU D 349 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 377 through 379 Processing sheet with id=AD7, first strand: chain 'D' and resid 475 through 480 Processing sheet with id=AD8, first strand: chain 'D' and resid 418 through 420 Processing sheet with id=AD9, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AE1, first strand: chain 'D' and resid 530 through 532 removed outlier: 4.085A pdb=" N ILE D 530 " --> pdb=" O TYR D 762 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 534 through 537 Processing sheet with id=AE3, first strand: chain 'H' and resid 4 through 8 removed outlier: 5.382A pdb=" N GLY H 16 " --> pdb=" O SER H 85 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.720A pdb=" N GLY H 10 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASN H 57 " --> pdb=" O ASN H 52 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AE6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.549A pdb=" N VAL L 13 " --> pdb=" O GLU L 109 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TRP L 39 " --> pdb=" O LEU L 51 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 4 through 8 removed outlier: 5.382A pdb=" N GLY M 16 " --> pdb=" O SER M 85 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR M 78 " --> pdb=" O ASP M 73 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP M 73 " --> pdb=" O THR M 78 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.720A pdb=" N GLY M 10 " --> pdb=" O THR M 116 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN M 57 " --> pdb=" O ASN M 52 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 5 through 7 Processing sheet with id=AF1, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.549A pdb=" N VAL N 13 " --> pdb=" O GLU N 109 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N TRP N 39 " --> pdb=" O LEU N 51 " (cutoff:3.500A) 1061 hydrogen bonds defined for protein. 2961 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.09 Time building geometry restraints manager: 2.68 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: 8941 1.34 - 1.46: 6395 1.46 - 1.58: 13067 1.58 - 1.70: 2 1.70 - 1.82: 294 Bond restraints: 28699 Sorted by residual: bond pdb=" CB GLU C 683 " pdb=" CG GLU C 683 " ideal model delta sigma weight residual 1.520 1.580 -0.060 3.00e-02 1.11e+03 3.97e+00 bond pdb=" CB GLU A 683 " pdb=" CG GLU A 683 " ideal model delta sigma weight residual 1.520 1.580 -0.060 3.00e-02 1.11e+03 3.97e+00 bond pdb=" CG LYS B 185 " pdb=" CD LYS B 185 " ideal model delta sigma weight residual 1.520 1.463 0.057 3.00e-02 1.11e+03 3.56e+00 bond pdb=" CB SER D 645 " pdb=" OG SER D 645 " ideal model delta sigma weight residual 1.417 1.380 0.037 2.00e-02 2.50e+03 3.45e+00 bond pdb=" C THR A 105 " pdb=" N PRO A 106 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.39e+00 ... (remaining 28694 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 38151 3.19 - 6.38: 614 6.38 - 9.57: 72 9.57 - 12.76: 8 12.76 - 15.95: 6 Bond angle restraints: 38851 Sorted by residual: angle pdb=" N ILE D 800 " pdb=" CA ILE D 800 " pdb=" C ILE D 800 " ideal model delta sigma weight residual 111.48 104.08 7.40 9.40e-01 1.13e+00 6.20e+01 angle pdb=" C ASP M 102 " pdb=" N GLY M 103 " pdb=" CA GLY M 103 " ideal model delta sigma weight residual 121.70 132.74 -11.04 1.80e+00 3.09e-01 3.76e+01 angle pdb=" C ASP H 102 " pdb=" N GLY H 103 " pdb=" CA GLY H 103 " ideal model delta sigma weight residual 121.70 132.71 -11.01 1.80e+00 3.09e-01 3.74e+01 angle pdb=" C LYS B 768 " pdb=" N ASP B 769 " pdb=" CA ASP B 769 " ideal model delta sigma weight residual 121.54 131.03 -9.49 1.91e+00 2.74e-01 2.47e+01 angle pdb=" N ASN D 803 " pdb=" CA ASN D 803 " pdb=" C ASN D 803 " ideal model delta sigma weight residual 110.80 121.34 -10.54 2.13e+00 2.20e-01 2.45e+01 ... (remaining 38846 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 15370 18.10 - 36.20: 1459 36.20 - 54.30: 236 54.30 - 72.39: 56 72.39 - 90.49: 18 Dihedral angle restraints: 17139 sinusoidal: 6833 harmonic: 10306 Sorted by residual: dihedral pdb=" CA HIS D 802 " pdb=" C HIS D 802 " pdb=" N ASN D 803 " pdb=" CA ASN D 803 " ideal model delta harmonic sigma weight residual -180.00 -120.98 -59.02 0 5.00e+00 4.00e-02 1.39e+02 dihedral pdb=" CA HIS B 802 " pdb=" C HIS B 802 " pdb=" N ASN B 803 " pdb=" CA ASN B 803 " ideal model delta harmonic sigma weight residual -180.00 -121.55 -58.45 0 5.00e+00 4.00e-02 1.37e+02 dihedral pdb=" CB CYS A 441 " pdb=" SG CYS A 441 " pdb=" SG CYS A 475 " pdb=" CB CYS A 475 " ideal model delta sinusoidal sigma weight residual -86.00 -176.49 90.49 1 1.00e+01 1.00e-02 9.68e+01 ... (remaining 17136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3602 0.079 - 0.159: 641 0.159 - 0.238: 68 0.238 - 0.317: 17 0.317 - 0.397: 5 Chirality restraints: 4333 Sorted by residual: chirality pdb=" CB VAL C 270 " pdb=" CA VAL C 270 " pdb=" CG1 VAL C 270 " pdb=" CG2 VAL C 270 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CB VAL A 270 " pdb=" CA VAL A 270 " pdb=" CG1 VAL A 270 " pdb=" CG2 VAL A 270 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CB ILE D 751 " pdb=" CA ILE D 751 " pdb=" CG1 ILE D 751 " pdb=" CG2 ILE D 751 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.60e+00 ... (remaining 4330 not shown) Planarity restraints: 4936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 679 " -0.063 5.00e-02 4.00e+02 9.62e-02 1.48e+01 pdb=" N PRO D 680 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO D 680 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO D 680 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO N 47 " 0.064 5.00e-02 4.00e+02 9.59e-02 1.47e+01 pdb=" N PRO N 48 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO N 48 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO N 48 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO L 47 " 0.064 5.00e-02 4.00e+02 9.59e-02 1.47e+01 pdb=" N PRO L 48 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO L 48 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO L 48 " 0.053 5.00e-02 4.00e+02 ... (remaining 4933 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4637 2.76 - 3.29: 26893 3.29 - 3.83: 49279 3.83 - 4.36: 55956 4.36 - 4.90: 89481 Nonbonded interactions: 226246 Sorted by model distance: nonbonded pdb=" OH TYR C 114 " pdb=" O CYS C 329 " model vdw 2.224 3.040 nonbonded pdb=" OH TYR A 114 " pdb=" O CYS A 329 " model vdw 2.225 3.040 nonbonded pdb=" O SER B 320 " pdb=" OG1 THR B 324 " model vdw 2.229 3.040 nonbonded pdb=" O SER D 320 " pdb=" OG1 THR D 324 " model vdw 2.234 3.040 nonbonded pdb=" O SER H 85 " pdb=" OG SER H 85 " model vdw 2.236 3.040 ... (remaining 226241 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 34 through 519 or resid 521 through 845)) } ncs_group { reference = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 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: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.200 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 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 : 0.005 0.069 28713 Z= 0.255 Angle : 1.034 15.948 38879 Z= 0.579 Chirality : 0.062 0.397 4333 Planarity : 0.008 0.096 4936 Dihedral : 14.450 82.866 10471 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.46 % Allowed : 10.63 % Favored : 88.91 % Rotamer: Outliers : 0.78 % Allowed : 8.47 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 4.48 % Twisted General : 1.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.42 (0.12), residues: 3509 helix: -3.09 (0.10), residues: 1156 sheet: -2.53 (0.20), residues: 534 loop : -2.96 (0.13), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 99 TYR 0.042 0.003 TYR D 823 PHE 0.037 0.003 PHE B 525 TRP 0.028 0.003 TRP C 657 HIS 0.019 0.003 HIS D 703 Details of bonding type rmsd covalent geometry : bond 0.00526 (28699) covalent geometry : angle 1.03348 (38851) SS BOND : bond 0.00297 ( 14) SS BOND : angle 1.97820 ( 28) hydrogen bonds : bond 0.18928 ( 1053) hydrogen bonds : angle 8.61725 ( 2961) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 HIS cc_start: 0.9103 (m170) cc_final: 0.8622 (t70) REVERT: A 155 MET cc_start: 0.9267 (mpp) cc_final: 0.8683 (mmp) REVERT: A 261 MET cc_start: 0.9450 (mmm) cc_final: 0.9081 (mmm) REVERT: A 576 MET cc_start: 0.9220 (mtp) cc_final: 0.8486 (tmm) REVERT: A 662 MET cc_start: 0.9742 (ppp) cc_final: 0.9295 (ppp) REVERT: A 751 ILE cc_start: 0.9848 (mt) cc_final: 0.9601 (tp) REVERT: B 307 MET cc_start: 0.9092 (ttp) cc_final: 0.8891 (tmm) REVERT: C 134 HIS cc_start: 0.9121 (m170) cc_final: 0.8539 (t70) REVERT: C 261 MET cc_start: 0.9462 (mmm) cc_final: 0.9111 (mmm) REVERT: C 576 MET cc_start: 0.9197 (mtp) cc_final: 0.8464 (tmm) REVERT: C 662 MET cc_start: 0.9741 (ppp) cc_final: 0.9294 (ppp) REVERT: C 751 ILE cc_start: 0.9841 (mt) cc_final: 0.9591 (tp) REVERT: D 307 MET cc_start: 0.8993 (ttp) cc_final: 0.8787 (tmm) REVERT: D 721 LEU cc_start: 0.9656 (OUTLIER) cc_final: 0.9389 (pt) REVERT: H 106 MET cc_start: 0.7778 (mpp) cc_final: 0.7457 (mpp) REVERT: N 58 LEU cc_start: 0.9539 (pp) cc_final: 0.9295 (mp) outliers start: 24 outliers final: 3 residues processed: 212 average time/residue: 0.1581 time to fit residues: 56.1142 Evaluate side-chains 159 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 155 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 HIS ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN A 362 ASN A 378 GLN A 425 HIS A 492 GLN A 515 ASN A 717 GLN A 763 GLN B 61 HIS B 118 GLN B 192 ASN B 649 ASN B 782 GLN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 HIS ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN C 362 ASN C 378 GLN C 425 HIS C 492 GLN C 515 ASN C 717 GLN C 763 GLN D 61 HIS D 118 GLN D 192 ASN D 649 ASN ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 782 GLN H 111 GLN ** L 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 111 GLN ** N 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.028201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.022889 restraints weight = 486919.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.023542 restraints weight = 302319.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.024008 restraints weight = 209523.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.024343 restraints weight = 159802.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.024607 restraints weight = 129495.631| |-----------------------------------------------------------------------------| r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28713 Z= 0.146 Angle : 0.674 7.671 38879 Z= 0.363 Chirality : 0.045 0.239 4333 Planarity : 0.005 0.091 4936 Dihedral : 7.016 50.383 3836 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.26 % Favored : 90.57 % Rotamer: Outliers : 0.13 % Allowed : 3.93 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 1.49 % Twisted General : 0.65 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.13), residues: 3509 helix: -1.17 (0.13), residues: 1168 sheet: -2.23 (0.20), residues: 598 loop : -2.72 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 139 TYR 0.019 0.002 TYR M 33 PHE 0.029 0.001 PHE D 525 TRP 0.013 0.001 TRP C 813 HIS 0.007 0.001 HIS D 703 Details of bonding type rmsd covalent geometry : bond 0.00300 (28699) covalent geometry : angle 0.67181 (38851) SS BOND : bond 0.00243 ( 14) SS BOND : angle 2.27918 ( 28) hydrogen bonds : bond 0.04146 ( 1053) hydrogen bonds : angle 6.35289 ( 2961) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 166 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.9643 (mmm) cc_final: 0.9389 (mmm) REVERT: A 523 MET cc_start: 0.9635 (mmm) cc_final: 0.8764 (mtp) REVERT: A 576 MET cc_start: 0.9235 (mtp) cc_final: 0.8490 (tmm) REVERT: A 751 ILE cc_start: 0.9806 (mt) cc_final: 0.9528 (tp) REVERT: B 132 MET cc_start: 0.8865 (ppp) cc_final: 0.8423 (ppp) REVERT: B 307 MET cc_start: 0.9113 (ttp) cc_final: 0.8810 (tmm) REVERT: B 497 MET cc_start: 0.9321 (mtm) cc_final: 0.9066 (mpp) REVERT: C 261 MET cc_start: 0.9657 (mmm) cc_final: 0.9175 (mmm) REVERT: C 523 MET cc_start: 0.9648 (mmm) cc_final: 0.8708 (mtp) REVERT: C 576 MET cc_start: 0.9243 (mtp) cc_final: 0.8494 (tmm) REVERT: D 132 MET cc_start: 0.8816 (ppp) cc_final: 0.8266 (ppp) REVERT: D 307 MET cc_start: 0.9036 (ttp) cc_final: 0.8742 (tmm) REVERT: D 497 MET cc_start: 0.9340 (mtm) cc_final: 0.9121 (mpp) REVERT: D 654 MET cc_start: 0.9492 (mmp) cc_final: 0.9101 (mmp) REVERT: H 106 MET cc_start: 0.8576 (mpp) cc_final: 0.8232 (mtm) REVERT: M 106 MET cc_start: 0.7986 (mmp) cc_final: 0.7757 (mmp) REVERT: N 51 LEU cc_start: 0.9587 (pt) cc_final: 0.9131 (pt) outliers start: 4 outliers final: 0 residues processed: 170 average time/residue: 0.1605 time to fit residues: 45.7666 Evaluate side-chains 144 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 343 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 175 optimal weight: 5.9990 chunk 193 optimal weight: 8.9990 chunk 266 optimal weight: 10.0000 chunk 157 optimal weight: 40.0000 chunk 258 optimal weight: 10.0000 chunk 195 optimal weight: 20.0000 chunk 286 optimal weight: 0.2980 chunk 223 optimal weight: 6.9990 chunk 136 optimal weight: 30.0000 overall best weight: 6.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 ASN A 378 GLN A 515 ASN B 54 HIS B 60 HIS ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 802 HIS ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 HIS D 60 HIS ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 78 ASN N 80 HIS ** N 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.026850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.021574 restraints weight = 501148.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.022196 restraints weight = 312965.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.022638 restraints weight = 222618.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.022962 restraints weight = 171828.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.023188 restraints weight = 140559.209| |-----------------------------------------------------------------------------| r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 28713 Z= 0.239 Angle : 0.729 9.452 38879 Z= 0.393 Chirality : 0.045 0.243 4333 Planarity : 0.005 0.089 4936 Dihedral : 6.885 42.472 3836 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.43 % Favored : 89.34 % Rotamer: Outliers : 0.16 % Allowed : 5.52 % Favored : 94.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.59 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.13), residues: 3509 helix: -0.41 (0.14), residues: 1170 sheet: -1.95 (0.21), residues: 572 loop : -2.72 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 327 TYR 0.025 0.002 TYR M 33 PHE 0.042 0.002 PHE D 144 TRP 0.018 0.002 TRP N 96 HIS 0.011 0.002 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00472 (28699) covalent geometry : angle 0.72732 (38851) SS BOND : bond 0.00234 ( 14) SS BOND : angle 1.83120 ( 28) hydrogen bonds : bond 0.04103 ( 1053) hydrogen bonds : angle 6.24172 ( 2961) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 160 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.9647 (mmm) cc_final: 0.9401 (mmm) REVERT: A 415 MET cc_start: 0.7955 (tpp) cc_final: 0.7600 (tpp) REVERT: A 523 MET cc_start: 0.9524 (mmm) cc_final: 0.8737 (mtp) REVERT: A 576 MET cc_start: 0.9178 (mtp) cc_final: 0.8508 (tmm) REVERT: A 839 MET cc_start: 0.8013 (ptp) cc_final: 0.7607 (mpp) REVERT: B 132 MET cc_start: 0.8834 (ppp) cc_final: 0.8523 (ppp) REVERT: B 307 MET cc_start: 0.9213 (ttp) cc_final: 0.8889 (tmm) REVERT: B 497 MET cc_start: 0.9289 (mtm) cc_final: 0.9001 (mpp) REVERT: B 654 MET cc_start: 0.9511 (mmp) cc_final: 0.9150 (mmp) REVERT: C 261 MET cc_start: 0.9644 (mmm) cc_final: 0.9413 (mmm) REVERT: C 415 MET cc_start: 0.7991 (tpp) cc_final: 0.7633 (tpp) REVERT: C 576 MET cc_start: 0.9215 (mtp) cc_final: 0.8512 (tmm) REVERT: C 839 MET cc_start: 0.8028 (ptp) cc_final: 0.7643 (mpp) REVERT: D 132 MET cc_start: 0.8815 (ppp) cc_final: 0.8399 (ppp) REVERT: D 307 MET cc_start: 0.9254 (ttp) cc_final: 0.8871 (tmm) REVERT: D 497 MET cc_start: 0.9300 (mtm) cc_final: 0.9070 (mpp) REVERT: D 654 MET cc_start: 0.9506 (mmp) cc_final: 0.9039 (mmm) REVERT: H 106 MET cc_start: 0.7973 (mpp) cc_final: 0.7473 (mpp) REVERT: M 83 MET cc_start: 0.8316 (mmp) cc_final: 0.8104 (mmm) REVERT: M 106 MET cc_start: 0.8121 (mmp) cc_final: 0.7919 (mmp) outliers start: 5 outliers final: 2 residues processed: 165 average time/residue: 0.1593 time to fit residues: 44.3903 Evaluate side-chains 146 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 144 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 104 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 188 optimal weight: 0.0010 chunk 56 optimal weight: 0.0980 chunk 122 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 240 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 chunk 230 optimal weight: 5.9990 chunk 340 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 ASN C 378 GLN D 323 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 HIS ** L 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 78 ASN ** N 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.027717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.022497 restraints weight = 487716.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.023140 restraints weight = 300600.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.023597 restraints weight = 207867.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.023922 restraints weight = 158041.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.024163 restraints weight = 128026.306| |-----------------------------------------------------------------------------| r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28713 Z= 0.127 Angle : 0.627 8.394 38879 Z= 0.336 Chirality : 0.045 0.305 4333 Planarity : 0.004 0.089 4936 Dihedral : 6.537 42.034 3836 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.75 % Favored : 90.08 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.14), residues: 3509 helix: 0.03 (0.15), residues: 1194 sheet: -1.95 (0.21), residues: 580 loop : -2.64 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 67 TYR 0.048 0.001 TYR M 33 PHE 0.037 0.001 PHE D 525 TRP 0.014 0.001 TRP N 96 HIS 0.009 0.001 HIS B 703 Details of bonding type rmsd covalent geometry : bond 0.00263 (28699) covalent geometry : angle 0.62485 (38851) SS BOND : bond 0.00240 ( 14) SS BOND : angle 2.07877 ( 28) hydrogen bonds : bond 0.03393 ( 1053) hydrogen bonds : angle 5.81554 ( 2961) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.9691 (mmm) cc_final: 0.9308 (mmm) REVERT: A 415 MET cc_start: 0.8011 (tpp) cc_final: 0.7606 (tpp) REVERT: A 457 CYS cc_start: 0.9158 (m) cc_final: 0.8933 (m) REVERT: A 576 MET cc_start: 0.9201 (mtp) cc_final: 0.8460 (tmm) REVERT: A 839 MET cc_start: 0.7933 (ptp) cc_final: 0.7533 (mpp) REVERT: B 132 MET cc_start: 0.8874 (ppp) cc_final: 0.8381 (ppp) REVERT: B 307 MET cc_start: 0.9163 (ttp) cc_final: 0.8824 (ppp) REVERT: B 497 MET cc_start: 0.9372 (mtm) cc_final: 0.9126 (mpp) REVERT: B 562 MET cc_start: 0.9648 (mmp) cc_final: 0.9443 (mmt) REVERT: B 654 MET cc_start: 0.9488 (mmp) cc_final: 0.9024 (mmp) REVERT: C 261 MET cc_start: 0.9701 (mmm) cc_final: 0.9319 (mmm) REVERT: C 375 MET cc_start: 0.9135 (mmp) cc_final: 0.8902 (mmp) REVERT: C 415 MET cc_start: 0.8214 (tpp) cc_final: 0.7812 (tpp) REVERT: C 457 CYS cc_start: 0.9197 (m) cc_final: 0.8960 (m) REVERT: C 523 MET cc_start: 0.9540 (mmm) cc_final: 0.8749 (mtp) REVERT: C 576 MET cc_start: 0.9225 (mtp) cc_final: 0.8452 (tmm) REVERT: C 839 MET cc_start: 0.7968 (ptp) cc_final: 0.7616 (mpp) REVERT: D 132 MET cc_start: 0.8905 (ppp) cc_final: 0.8431 (ppp) REVERT: D 307 MET cc_start: 0.9195 (ttp) cc_final: 0.8838 (tmm) REVERT: D 654 MET cc_start: 0.9485 (mmp) cc_final: 0.9035 (mmm) REVERT: D 789 MET cc_start: 0.9418 (ptp) cc_final: 0.9189 (mpp) REVERT: D 809 MET cc_start: 0.9079 (mmt) cc_final: 0.8779 (mmm) REVERT: M 83 MET cc_start: 0.8495 (mmp) cc_final: 0.8272 (mmm) REVERT: N 37 MET cc_start: 0.8564 (tmm) cc_final: 0.8289 (tmm) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1619 time to fit residues: 43.2554 Evaluate side-chains 145 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 241 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 341 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 284 optimal weight: 20.0000 chunk 54 optimal weight: 0.0040 chunk 287 optimal weight: 3.9990 chunk 34 optimal weight: 0.0070 chunk 157 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 chunk 229 optimal weight: 2.9990 overall best weight: 2.6016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 HIS ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 94 HIS ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 94 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.027718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.022487 restraints weight = 488485.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.023141 restraints weight = 298445.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.023592 restraints weight = 206508.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.023929 restraints weight = 157364.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.024163 restraints weight = 127410.303| |-----------------------------------------------------------------------------| r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 28713 Z= 0.128 Angle : 0.628 16.673 38879 Z= 0.334 Chirality : 0.044 0.215 4333 Planarity : 0.004 0.089 4936 Dihedral : 6.381 39.657 3836 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.49 % Favored : 90.34 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.14), residues: 3509 helix: 0.29 (0.15), residues: 1191 sheet: -1.94 (0.21), residues: 576 loop : -2.55 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 99 TYR 0.041 0.001 TYR M 33 PHE 0.048 0.001 PHE B 144 TRP 0.012 0.001 TRP C 402 HIS 0.008 0.001 HIS D 703 Details of bonding type rmsd covalent geometry : bond 0.00269 (28699) covalent geometry : angle 0.62467 (38851) SS BOND : bond 0.00273 ( 14) SS BOND : angle 2.40173 ( 28) hydrogen bonds : bond 0.03283 ( 1053) hydrogen bonds : angle 5.70395 ( 2961) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.9699 (mmm) cc_final: 0.9304 (mmm) REVERT: A 375 MET cc_start: 0.8742 (tpt) cc_final: 0.7998 (mmm) REVERT: A 415 MET cc_start: 0.8236 (tpp) cc_final: 0.7817 (tpp) REVERT: A 523 MET cc_start: 0.9725 (mmm) cc_final: 0.8914 (mtp) REVERT: A 576 MET cc_start: 0.9190 (mtp) cc_final: 0.8474 (tmm) REVERT: A 839 MET cc_start: 0.7965 (ptp) cc_final: 0.7599 (mpp) REVERT: B 132 MET cc_start: 0.8934 (ppp) cc_final: 0.8432 (ppp) REVERT: B 497 MET cc_start: 0.9345 (mtm) cc_final: 0.9115 (mpp) REVERT: B 565 MET cc_start: 0.9704 (mtm) cc_final: 0.9483 (ptp) REVERT: B 654 MET cc_start: 0.9493 (mmp) cc_final: 0.9028 (mmm) REVERT: C 261 MET cc_start: 0.9707 (mmm) cc_final: 0.9306 (mmm) REVERT: C 415 MET cc_start: 0.8281 (tpp) cc_final: 0.7868 (tpp) REVERT: C 523 MET cc_start: 0.9534 (mmm) cc_final: 0.8772 (mtp) REVERT: C 576 MET cc_start: 0.9227 (mtp) cc_final: 0.8470 (tmm) REVERT: C 839 MET cc_start: 0.7992 (ptp) cc_final: 0.7639 (mpp) REVERT: D 132 MET cc_start: 0.8915 (ppp) cc_final: 0.8448 (ppp) REVERT: D 307 MET cc_start: 0.9184 (ttp) cc_final: 0.8908 (ppp) REVERT: D 654 MET cc_start: 0.9496 (mmp) cc_final: 0.9036 (mmm) REVERT: D 809 MET cc_start: 0.8993 (mmt) cc_final: 0.8698 (mmm) REVERT: H 83 MET cc_start: 0.7259 (tpt) cc_final: 0.6993 (tpp) REVERT: M 83 MET cc_start: 0.8634 (mmp) cc_final: 0.8217 (mpp) REVERT: M 106 MET cc_start: 0.7969 (mmp) cc_final: 0.7643 (mmp) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1643 time to fit residues: 43.7718 Evaluate side-chains 146 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 198 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 chunk 346 optimal weight: 0.9980 chunk 237 optimal weight: 0.1980 chunk 188 optimal weight: 8.9990 chunk 178 optimal weight: 6.9990 chunk 350 optimal weight: 10.0000 chunk 205 optimal weight: 10.0000 chunk 296 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 100 optimal weight: 30.0000 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 GLN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 748 HIS D 737 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** 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 = 0.2936 r_free = 0.2936 target = 0.027760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.022526 restraints weight = 487936.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.023173 restraints weight = 300056.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.023631 restraints weight = 208619.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.023961 restraints weight = 159251.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.024193 restraints weight = 129283.341| |-----------------------------------------------------------------------------| r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28713 Z= 0.128 Angle : 0.615 13.777 38879 Z= 0.327 Chirality : 0.044 0.255 4333 Planarity : 0.004 0.082 4936 Dihedral : 6.217 38.856 3836 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.60 % Favored : 90.17 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.14), residues: 3509 helix: 0.41 (0.15), residues: 1193 sheet: -1.95 (0.21), residues: 566 loop : -2.54 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 692 TYR 0.036 0.001 TYR M 33 PHE 0.033 0.001 PHE B 144 TRP 0.013 0.001 TRP C 402 HIS 0.007 0.001 HIS D 703 Details of bonding type rmsd covalent geometry : bond 0.00269 (28699) covalent geometry : angle 0.61246 (38851) SS BOND : bond 0.00244 ( 14) SS BOND : angle 2.30535 ( 28) hydrogen bonds : bond 0.03198 ( 1053) hydrogen bonds : angle 5.55126 ( 2961) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.9444 (tpt) cc_final: 0.9239 (tpt) REVERT: A 261 MET cc_start: 0.9690 (mmm) cc_final: 0.9338 (mmm) REVERT: A 375 MET cc_start: 0.9157 (tpt) cc_final: 0.8762 (mmm) REVERT: A 415 MET cc_start: 0.8246 (tpp) cc_final: 0.7835 (tpp) REVERT: A 523 MET cc_start: 0.9586 (mmm) cc_final: 0.8821 (mtp) REVERT: A 576 MET cc_start: 0.9224 (mtp) cc_final: 0.8471 (tmm) REVERT: B 132 MET cc_start: 0.8926 (ppp) cc_final: 0.8460 (ppp) REVERT: B 497 MET cc_start: 0.9347 (mtm) cc_final: 0.9121 (mpp) REVERT: B 565 MET cc_start: 0.9795 (mtm) cc_final: 0.9590 (mtt) REVERT: B 654 MET cc_start: 0.9501 (mmp) cc_final: 0.9070 (mmm) REVERT: C 155 MET cc_start: 0.9025 (mmp) cc_final: 0.8464 (tpt) REVERT: C 261 MET cc_start: 0.9703 (mmm) cc_final: 0.9333 (mmm) REVERT: C 415 MET cc_start: 0.8293 (tpp) cc_final: 0.7894 (tpp) REVERT: C 523 MET cc_start: 0.9565 (mmm) cc_final: 0.8764 (mtp) REVERT: C 576 MET cc_start: 0.9240 (mtp) cc_final: 0.8478 (tmm) REVERT: D 132 MET cc_start: 0.8986 (ppp) cc_final: 0.8563 (ppp) REVERT: D 654 MET cc_start: 0.9497 (mmp) cc_final: 0.9074 (mmm) REVERT: D 789 MET cc_start: 0.9480 (ptp) cc_final: 0.9242 (pmm) REVERT: D 809 MET cc_start: 0.9112 (mmt) cc_final: 0.8808 (mmm) REVERT: M 83 MET cc_start: 0.8503 (mmp) cc_final: 0.8133 (mpp) REVERT: M 106 MET cc_start: 0.7857 (mmp) cc_final: 0.7557 (mmp) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1615 time to fit residues: 42.9212 Evaluate side-chains 144 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 339 optimal weight: 8.9990 chunk 186 optimal weight: 3.9990 chunk 241 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 351 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 5.9990 chunk 178 optimal weight: 8.9990 chunk 161 optimal weight: 4.9990 chunk 198 optimal weight: 8.9990 chunk 193 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS B 323 ASN ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 737 ASN ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 HIS ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 ASN D 802 HIS ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.026593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.021367 restraints weight = 500037.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.021973 restraints weight = 314431.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.022403 restraints weight = 222749.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.022700 restraints weight = 172357.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.022937 restraints weight = 142516.303| |-----------------------------------------------------------------------------| r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 28713 Z= 0.232 Angle : 0.708 9.481 38879 Z= 0.379 Chirality : 0.045 0.235 4333 Planarity : 0.005 0.081 4936 Dihedral : 6.519 39.692 3836 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 21.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.72 % Favored : 89.11 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.56 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.14), residues: 3509 helix: 0.25 (0.15), residues: 1202 sheet: -2.01 (0.21), residues: 549 loop : -2.63 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 337 TYR 0.030 0.002 TYR M 33 PHE 0.032 0.002 PHE D 525 TRP 0.015 0.002 TRP H 109 HIS 0.014 0.002 HIS C 748 Details of bonding type rmsd covalent geometry : bond 0.00464 (28699) covalent geometry : angle 0.70456 (38851) SS BOND : bond 0.00465 ( 14) SS BOND : angle 2.53817 ( 28) hydrogen bonds : bond 0.03632 ( 1053) hydrogen bonds : angle 5.82119 ( 2961) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.9433 (tpt) cc_final: 0.9123 (tpt) REVERT: A 261 MET cc_start: 0.9720 (mmm) cc_final: 0.9369 (mmm) REVERT: A 415 MET cc_start: 0.8167 (tpp) cc_final: 0.7772 (tpp) REVERT: A 523 MET cc_start: 0.9557 (mmm) cc_final: 0.8780 (mtp) REVERT: A 576 MET cc_start: 0.9267 (mtp) cc_final: 0.8539 (tmm) REVERT: A 839 MET cc_start: 0.8343 (ptp) cc_final: 0.8118 (mpp) REVERT: B 565 MET cc_start: 0.9849 (mtm) cc_final: 0.9524 (mtm) REVERT: B 654 MET cc_start: 0.9530 (mmp) cc_final: 0.9234 (mmp) REVERT: B 809 MET cc_start: 0.8954 (mmt) cc_final: 0.8593 (mmm) REVERT: C 230 MET cc_start: 0.9440 (tpt) cc_final: 0.9102 (tpt) REVERT: C 261 MET cc_start: 0.9726 (mmm) cc_final: 0.9481 (mmm) REVERT: C 415 MET cc_start: 0.8340 (tpp) cc_final: 0.7956 (tpp) REVERT: C 523 MET cc_start: 0.9558 (mmm) cc_final: 0.8784 (mtp) REVERT: C 576 MET cc_start: 0.9308 (mtp) cc_final: 0.8603 (tmm) REVERT: C 839 MET cc_start: 0.8369 (ptp) cc_final: 0.8140 (mpp) REVERT: D 654 MET cc_start: 0.9535 (mmp) cc_final: 0.9257 (mmm) REVERT: M 83 MET cc_start: 0.8595 (mmp) cc_final: 0.8234 (mpp) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1580 time to fit residues: 41.3702 Evaluate side-chains 140 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 66 optimal weight: 0.0870 chunk 278 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 315 optimal weight: 8.9990 chunk 154 optimal weight: 40.0000 chunk 288 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 13 optimal weight: 20.0000 chunk 259 optimal weight: 10.0000 chunk 94 optimal weight: 20.0000 chunk 242 optimal weight: 4.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 ASN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.027531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.022327 restraints weight = 492170.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.022967 restraints weight = 298876.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.023413 restraints weight = 208843.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.023736 restraints weight = 160595.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.023965 restraints weight = 130461.134| |-----------------------------------------------------------------------------| r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28713 Z= 0.133 Angle : 0.634 9.481 38879 Z= 0.337 Chirality : 0.044 0.245 4333 Planarity : 0.004 0.081 4936 Dihedral : 6.311 40.152 3836 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.40 % Favored : 90.42 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.47 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.14), residues: 3509 helix: 0.44 (0.15), residues: 1218 sheet: -1.85 (0.21), residues: 530 loop : -2.61 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 65 TYR 0.053 0.001 TYR M 33 PHE 0.029 0.001 PHE D 144 TRP 0.043 0.002 TRP D 166 HIS 0.007 0.001 HIS D 703 Details of bonding type rmsd covalent geometry : bond 0.00281 (28699) covalent geometry : angle 0.63066 (38851) SS BOND : bond 0.01275 ( 14) SS BOND : angle 2.67039 ( 28) hydrogen bonds : bond 0.03224 ( 1053) hydrogen bonds : angle 5.53830 ( 2961) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8896 (mmp) cc_final: 0.8603 (mmp) REVERT: A 230 MET cc_start: 0.9331 (tpt) cc_final: 0.9034 (tpt) REVERT: A 261 MET cc_start: 0.9700 (mmm) cc_final: 0.9290 (mmm) REVERT: A 375 MET cc_start: 0.9149 (mmp) cc_final: 0.8859 (tpp) REVERT: A 415 MET cc_start: 0.8278 (tpp) cc_final: 0.7918 (tpp) REVERT: A 523 MET cc_start: 0.9569 (mmm) cc_final: 0.8863 (mtp) REVERT: A 576 MET cc_start: 0.9218 (mtp) cc_final: 0.8536 (tmm) REVERT: A 839 MET cc_start: 0.8396 (ptp) cc_final: 0.8141 (mpp) REVERT: B 654 MET cc_start: 0.9522 (mmp) cc_final: 0.9153 (mmm) REVERT: B 809 MET cc_start: 0.9144 (mmt) cc_final: 0.8707 (mmm) REVERT: C 155 MET cc_start: 0.8912 (mmp) cc_final: 0.8608 (mmp) REVERT: C 230 MET cc_start: 0.9348 (tpt) cc_final: 0.9131 (tpt) REVERT: C 261 MET cc_start: 0.9707 (mmm) cc_final: 0.9288 (mmm) REVERT: C 375 MET cc_start: 0.9030 (mmm) cc_final: 0.8213 (mmm) REVERT: C 415 MET cc_start: 0.8312 (tpp) cc_final: 0.7963 (tpp) REVERT: C 523 MET cc_start: 0.9558 (mmm) cc_final: 0.8806 (mtp) REVERT: C 576 MET cc_start: 0.9248 (mtp) cc_final: 0.8557 (tmm) REVERT: C 839 MET cc_start: 0.8375 (ptp) cc_final: 0.8071 (mpp) REVERT: D 537 MET cc_start: 0.8880 (tpt) cc_final: 0.8648 (tpp) REVERT: D 654 MET cc_start: 0.9520 (mmp) cc_final: 0.9235 (mmp) REVERT: D 789 MET cc_start: 0.9499 (ptp) cc_final: 0.9209 (pmm) REVERT: D 809 MET cc_start: 0.8955 (mmt) cc_final: 0.8680 (mmm) REVERT: H 83 MET cc_start: 0.7167 (tpt) cc_final: 0.6964 (tpp) REVERT: M 83 MET cc_start: 0.8598 (mmp) cc_final: 0.8228 (mpp) REVERT: M 106 MET cc_start: 0.7787 (mmp) cc_final: 0.7311 (mmp) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1517 time to fit residues: 39.0628 Evaluate side-chains 139 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 86 optimal weight: 8.9990 chunk 298 optimal weight: 9.9990 chunk 243 optimal weight: 7.9990 chunk 342 optimal weight: 40.0000 chunk 116 optimal weight: 20.0000 chunk 300 optimal weight: 6.9990 chunk 34 optimal weight: 30.0000 chunk 172 optimal weight: 9.9990 chunk 267 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 344 optimal weight: 5.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 ASN B 694 ASN ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** 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 = 0.2864 r_free = 0.2864 target = 0.026101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.020926 restraints weight = 507913.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.021523 restraints weight = 316742.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.021948 restraints weight = 225925.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.022252 restraints weight = 175262.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.022466 restraints weight = 144325.876| |-----------------------------------------------------------------------------| r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 28713 Z= 0.275 Angle : 0.777 10.748 38879 Z= 0.415 Chirality : 0.046 0.227 4333 Planarity : 0.005 0.082 4936 Dihedral : 6.730 39.657 3836 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 25.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.40 % Favored : 88.43 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.56 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.14), residues: 3509 helix: 0.04 (0.15), residues: 1212 sheet: -1.91 (0.22), residues: 504 loop : -2.70 (0.14), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 98 TYR 0.048 0.002 TYR M 33 PHE 0.049 0.002 PHE B 525 TRP 0.030 0.003 TRP B 166 HIS 0.014 0.002 HIS C 748 Details of bonding type rmsd covalent geometry : bond 0.00551 (28699) covalent geometry : angle 0.77308 (38851) SS BOND : bond 0.00369 ( 14) SS BOND : angle 2.86858 ( 28) hydrogen bonds : bond 0.03927 ( 1053) hydrogen bonds : angle 5.99634 ( 2961) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8980 (mmp) cc_final: 0.8735 (mmp) REVERT: A 230 MET cc_start: 0.9425 (tpt) cc_final: 0.9144 (tpt) REVERT: A 261 MET cc_start: 0.9709 (mmm) cc_final: 0.9500 (mmm) REVERT: A 415 MET cc_start: 0.8230 (tpp) cc_final: 0.7880 (tpp) REVERT: A 523 MET cc_start: 0.9558 (mmm) cc_final: 0.8759 (mtp) REVERT: A 576 MET cc_start: 0.9269 (mtp) cc_final: 0.8649 (tmm) REVERT: A 655 MET cc_start: 0.8306 (tpp) cc_final: 0.8074 (tpp) REVERT: A 839 MET cc_start: 0.8419 (ptp) cc_final: 0.8170 (mpp) REVERT: B 89 MET cc_start: 0.9170 (mmm) cc_final: 0.8950 (tpp) REVERT: B 565 MET cc_start: 0.9877 (mtm) cc_final: 0.9662 (ptp) REVERT: B 654 MET cc_start: 0.9531 (mmp) cc_final: 0.9227 (mmp) REVERT: C 155 MET cc_start: 0.8982 (mmp) cc_final: 0.8758 (mmp) REVERT: C 230 MET cc_start: 0.9433 (tpt) cc_final: 0.9127 (tpt) REVERT: C 261 MET cc_start: 0.9712 (mmm) cc_final: 0.9491 (mmm) REVERT: C 415 MET cc_start: 0.8248 (tpp) cc_final: 0.7907 (tpp) REVERT: C 523 MET cc_start: 0.9563 (mmm) cc_final: 0.8829 (mmm) REVERT: C 576 MET cc_start: 0.9295 (mtp) cc_final: 0.8649 (tmm) REVERT: C 839 MET cc_start: 0.8404 (ptp) cc_final: 0.8157 (mpp) REVERT: D 537 MET cc_start: 0.8998 (tpt) cc_final: 0.8696 (tpp) REVERT: D 654 MET cc_start: 0.9531 (mmp) cc_final: 0.9263 (mmm) REVERT: D 789 MET cc_start: 0.9530 (ptp) cc_final: 0.9225 (pmm) REVERT: M 83 MET cc_start: 0.8670 (mmp) cc_final: 0.8408 (mpp) REVERT: M 106 MET cc_start: 0.7859 (mmp) cc_final: 0.7441 (mmp) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1692 time to fit residues: 43.1296 Evaluate side-chains 140 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 75 optimal weight: 20.0000 chunk 236 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 175 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 246 optimal weight: 0.6980 chunk 249 optimal weight: 7.9990 chunk 176 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.027315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.022194 restraints weight = 489456.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.022834 restraints weight = 299679.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.023284 restraints weight = 207017.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.023608 restraints weight = 157491.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.023843 restraints weight = 127925.769| |-----------------------------------------------------------------------------| r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 28713 Z= 0.125 Angle : 0.652 10.437 38879 Z= 0.344 Chirality : 0.045 0.244 4333 Planarity : 0.004 0.083 4936 Dihedral : 6.370 38.297 3836 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.55 % Favored : 90.28 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.14), residues: 3509 helix: 0.36 (0.15), residues: 1218 sheet: -1.91 (0.22), residues: 520 loop : -2.58 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 24 TYR 0.046 0.002 TYR M 33 PHE 0.037 0.002 PHE D 525 TRP 0.027 0.002 TRP D 166 HIS 0.007 0.001 HIS A 748 Details of bonding type rmsd covalent geometry : bond 0.00269 (28699) covalent geometry : angle 0.64694 (38851) SS BOND : bond 0.00319 ( 14) SS BOND : angle 3.13874 ( 28) hydrogen bonds : bond 0.03245 ( 1053) hydrogen bonds : angle 5.59148 ( 2961) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7018 Ramachandran restraints generated. 3509 Oldfield, 0 Emsley, 3509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.9019 (mmp) cc_final: 0.8735 (mmp) REVERT: A 230 MET cc_start: 0.9391 (tpt) cc_final: 0.9072 (tpt) REVERT: A 261 MET cc_start: 0.9694 (mmm) cc_final: 0.9312 (mmm) REVERT: A 415 MET cc_start: 0.8609 (tpp) cc_final: 0.8389 (tpp) REVERT: A 523 MET cc_start: 0.9594 (mmm) cc_final: 0.8865 (mtp) REVERT: A 576 MET cc_start: 0.9243 (mtp) cc_final: 0.8540 (tmm) REVERT: A 655 MET cc_start: 0.8177 (tpp) cc_final: 0.7914 (tpp) REVERT: A 839 MET cc_start: 0.8412 (ptp) cc_final: 0.8181 (mpp) REVERT: B 654 MET cc_start: 0.9496 (mmp) cc_final: 0.9161 (mmp) REVERT: B 809 MET cc_start: 0.9141 (mmt) cc_final: 0.8939 (mmm) REVERT: C 155 MET cc_start: 0.9014 (mmp) cc_final: 0.8736 (mmp) REVERT: C 230 MET cc_start: 0.9424 (tpt) cc_final: 0.9106 (tpt) REVERT: C 261 MET cc_start: 0.9702 (mmm) cc_final: 0.9314 (mmm) REVERT: C 415 MET cc_start: 0.8550 (tpp) cc_final: 0.8286 (tpp) REVERT: C 523 MET cc_start: 0.9577 (mmm) cc_final: 0.8805 (mtp) REVERT: C 576 MET cc_start: 0.9207 (mtp) cc_final: 0.8412 (tmm) REVERT: C 839 MET cc_start: 0.8381 (ptp) cc_final: 0.8112 (mpp) REVERT: D 537 MET cc_start: 0.8906 (tpt) cc_final: 0.8671 (tpp) REVERT: D 654 MET cc_start: 0.9514 (mmp) cc_final: 0.9180 (mmp) REVERT: D 789 MET cc_start: 0.9449 (ptp) cc_final: 0.9128 (pmm) REVERT: L 37 MET cc_start: 0.8659 (tmm) cc_final: 0.8455 (tpp) REVERT: M 83 MET cc_start: 0.8647 (mmp) cc_final: 0.8341 (mpp) REVERT: M 106 MET cc_start: 0.7957 (mmp) cc_final: 0.7593 (mmp) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1679 time to fit residues: 42.5060 Evaluate side-chains 139 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 217 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 254 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 0.0670 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.027149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.022037 restraints weight = 494222.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.022664 restraints weight = 299086.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.023111 restraints weight = 208814.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.023421 restraints weight = 159437.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.023656 restraints weight = 130455.657| |-----------------------------------------------------------------------------| r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28713 Z= 0.140 Angle : 0.644 9.745 38879 Z= 0.341 Chirality : 0.044 0.225 4333 Planarity : 0.004 0.083 4936 Dihedral : 6.252 37.486 3836 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.17 % Favored : 89.66 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.14), residues: 3509 helix: 0.42 (0.15), residues: 1215 sheet: -1.84 (0.21), residues: 540 loop : -2.55 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 24 TYR 0.045 0.001 TYR M 33 PHE 0.033 0.002 PHE D 525 TRP 0.023 0.002 TRP D 166 HIS 0.007 0.001 HIS A 748 Details of bonding type rmsd covalent geometry : bond 0.00294 (28699) covalent geometry : angle 0.63967 (38851) SS BOND : bond 0.00249 ( 14) SS BOND : angle 2.96222 ( 28) hydrogen bonds : bond 0.03184 ( 1053) hydrogen bonds : angle 5.53409 ( 2961) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3744.17 seconds wall clock time: 66 minutes 11.33 seconds (3971.33 seconds total)