Starting phenix.real_space_refine on Tue Jun 24 07:04:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tet_25852/06_2025/7tet_25852.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tet_25852/06_2025/7tet_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_25852/06_2025/7tet_25852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tet_25852/06_2025/7tet_25852.map" model { file = "/net/cci-nas-00/data/ceres_data/7tet_25852/06_2025/7tet_25852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tet_25852/06_2025/7tet_25852.cif" } resolution = 4.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.044 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.77, per 1000 atoms: 0.60 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: 7.15 Conformation dependent library (CDL) restraints added in 3.6 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: 3.71 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: 12.05 Time building geometry restraints manager: 8.31 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: 1.280 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: 0.020 Extract box with map and model: 1.140 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 64.940 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.290 ------------------------------------------------------------------------------- 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 : 9.44 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.42 (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 TRP 0.028 0.003 TRP C 657 HIS 0.019 0.003 HIS D 703 PHE 0.037 0.003 PHE B 525 TYR 0.042 0.003 TYR D 823 ARG 0.010 0.001 ARG H 99 Details of bonding type rmsd hydrogen bonds : bond 0.18928 ( 1053) hydrogen bonds : angle 8.61725 ( 2961) SS BOND : bond 0.00297 ( 14) SS BOND : angle 1.97820 ( 28) covalent geometry : bond 0.00526 (28699) covalent geometry : angle 1.03348 (38851) *********************** 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 : 3.393 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: 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: 0.8487 (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: C 134 HIS cc_start: 0.9121 (m170) cc_final: 0.8539 (t70) REVERT: C 261 MET cc_start: 0.9462 (mmm) cc_final: 0.9110 (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 721 LEU cc_start: 0.9656 (OUTLIER) cc_final: 0.9388 (pt) REVERT: H 106 MET cc_start: 0.7779 (mpp) cc_final: 0.7458 (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: 0.3772 time to fit residues: 132.3014 Evaluate side-chains 160 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 156 time to evaluate : 3.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 298 optimal weight: 8.9990 chunk 267 optimal weight: 20.0000 chunk 148 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 chunk 142 optimal weight: 2.9990 chunk 276 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 205 optimal weight: 8.9990 chunk 320 optimal weight: 40.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 134 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 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 ASN B 649 ASN ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 782 GLN ** B 802 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 HIS C 134 HIS ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN C 362 ASN C 378 GLN ** C 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 GLN ** L 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 111 GLN N 80 HIS ** N 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.027212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.021941 restraints weight = 492656.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.022567 restraints weight = 310124.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.023021 restraints weight = 218100.240| |-----------------------------------------------------------------------------| r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28713 Z= 0.220 Angle : 0.745 9.929 38879 Z= 0.402 Chirality : 0.046 0.213 4333 Planarity : 0.006 0.093 4936 Dihedral : 7.212 51.747 3836 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.69 % Favored : 90.14 % Rotamer: Outliers : 0.13 % Allowed : 4.93 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 1.49 % Twisted General : 0.65 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.13), residues: 3509 helix: -1.22 (0.13), residues: 1169 sheet: -2.19 (0.21), residues: 580 loop : -2.71 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 96 HIS 0.006 0.002 HIS D 703 PHE 0.031 0.002 PHE D 525 TYR 0.017 0.002 TYR D 705 ARG 0.006 0.001 ARG A 411 Details of bonding type rmsd hydrogen bonds : bond 0.04665 ( 1053) hydrogen bonds : angle 6.50807 ( 2961) SS BOND : bond 0.00259 ( 14) SS BOND : angle 2.66089 ( 28) covalent geometry : bond 0.00443 (28699) covalent geometry : angle 0.74211 (38851) *********************** 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 165 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 161 time to evaluate : 3.654 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: 0.9636 (mmm) cc_final: 0.9401 (mmm) REVERT: A 523 MET cc_start: 0.9683 (mmm) cc_final: 0.8953 (mtp) REVERT: A 576 MET cc_start: 0.9171 (mtp) cc_final: 0.8504 (tmm) REVERT: B 132 MET cc_start: 0.8920 (ppp) cc_final: 0.8517 (ppp) REVERT: B 497 MET cc_start: 0.9302 (mtm) cc_final: 0.9027 (mpp) REVERT: B 508 MET cc_start: 0.8921 (ttm) cc_final: 0.8642 (tpp) REVERT: B 654 MET cc_start: 0.9566 (mmp) cc_final: 0.9287 (mmm) REVERT: C 261 MET cc_start: 0.9627 (mmm) cc_final: 0.9396 (mmm) REVERT: C 523 MET cc_start: 0.9669 (mmm) cc_final: 0.8750 (mtp) REVERT: C 576 MET cc_start: 0.9165 (mtp) cc_final: 0.8494 (tmm) REVERT: D 132 MET cc_start: 0.8859 (ppp) cc_final: 0.8332 (ppp) REVERT: D 497 MET cc_start: 0.9301 (mtm) cc_final: 0.9047 (mpp) REVERT: D 654 MET cc_start: 0.9561 (mmp) cc_final: 0.9251 (mmm) REVERT: H 33 TYR cc_start: 0.8879 (t80) cc_final: 0.8608 (t80) REVERT: H 106 MET cc_start: 0.7994 (mpp) cc_final: 0.7429 (tpp) REVERT: M 106 MET cc_start: 0.8121 (mmp) cc_final: 0.7860 (mmp) outliers start: 4 outliers final: 0 residues processed: 165 average time/residue: 0.3830 time to fit residues: 105.3168 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 : 3.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 193 optimal weight: 40.0000 chunk 297 optimal weight: 6.9990 chunk 301 optimal weight: 9.9990 chunk 218 optimal weight: 9.9990 chunk 311 optimal weight: 0.7980 chunk 147 optimal weight: 0.2980 chunk 171 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 233 optimal weight: 0.0040 chunk 202 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 overall best weight: 2.4196 ------------------------------------------------------------------------------- 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** A 376 ASN A 378 GLN B 60 HIS B 118 GLN ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 802 HIS ** 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 60 HIS D 323 ASN ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 782 GLN ** 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 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.028066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.022784 restraints weight = 482509.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.023442 restraints weight = 294106.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.023904 restraints weight = 205157.812| |-----------------------------------------------------------------------------| r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2222 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= 0.124 Angle : 0.633 11.944 38879 Z= 0.341 Chirality : 0.045 0.204 4333 Planarity : 0.005 0.088 4936 Dihedral : 6.695 44.038 3836 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.92 % Favored : 90.91 % Rotamer: Outliers : 0.06 % Allowed : 3.93 % Favored : 96.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.56 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.14), residues: 3509 helix: -0.37 (0.14), residues: 1177 sheet: -1.93 (0.21), residues: 584 loop : -2.70 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 96 HIS 0.007 0.001 HIS B 703 PHE 0.030 0.001 PHE B 525 TYR 0.046 0.001 TYR H 33 ARG 0.006 0.000 ARG H 67 Details of bonding type rmsd hydrogen bonds : bond 0.03653 ( 1053) hydrogen bonds : angle 5.98875 ( 2961) SS BOND : bond 0.00235 ( 14) SS BOND : angle 1.80427 ( 28) covalent geometry : bond 0.00258 (28699) covalent geometry : angle 0.63177 (38851) *********************** 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 162 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 3.281 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: A 261 MET cc_start: 0.9689 (mmm) cc_final: 0.9265 (mmm) REVERT: A 523 MET cc_start: 0.9512 (mmm) cc_final: 0.8742 (mtp) REVERT: A 576 MET cc_start: 0.9255 (mtp) cc_final: 0.8530 (tmm) REVERT: A 839 MET cc_start: 0.7796 (ptp) cc_final: 0.7408 (mpp) REVERT: B 132 MET cc_start: 0.8911 (ppp) cc_final: 0.8422 (ppp) REVERT: B 497 MET cc_start: 0.9347 (mtm) cc_final: 0.9043 (mpp) REVERT: B 654 MET cc_start: 0.9513 (mmp) cc_final: 0.9141 (mmp) REVERT: B 809 MET cc_start: 0.8908 (tpp) cc_final: 0.8583 (mmm) REVERT: C 261 MET cc_start: 0.9685 (mmm) cc_final: 0.9208 (mmm) REVERT: C 415 MET cc_start: 0.8575 (tpp) cc_final: 0.8367 (tpp) REVERT: C 523 MET cc_start: 0.9525 (mmm) cc_final: 0.8756 (mtp) REVERT: C 576 MET cc_start: 0.9285 (mtp) cc_final: 0.8528 (tmm) REVERT: C 839 MET cc_start: 0.7820 (ptp) cc_final: 0.7455 (mpp) REVERT: D 132 MET cc_start: 0.8866 (ppp) cc_final: 0.8345 (ppp) REVERT: D 497 MET cc_start: 0.9336 (mtm) cc_final: 0.9099 (mpp) REVERT: D 654 MET cc_start: 0.9487 (mmp) cc_final: 0.9090 (mmp) REVERT: H 83 MET cc_start: 0.7500 (tpt) cc_final: 0.7257 (tpp) REVERT: N 41 GLN cc_start: 0.8534 (pt0) cc_final: 0.8270 (pm20) outliers start: 2 outliers final: 2 residues processed: 162 average time/residue: 0.3857 time to fit residues: 104.0212 Evaluate side-chains 147 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 3.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 121 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 203 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 139 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 269 optimal weight: 0.0970 chunk 134 optimal weight: 20.0000 chunk 274 optimal weight: 5.9990 chunk 158 optimal weight: 10.0000 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 54 HIS B 323 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 HIS ** D 767 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.026812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.020231 restraints weight = 457014.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.020896 restraints weight = 296909.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.021385 restraints weight = 219121.207| |-----------------------------------------------------------------------------| r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 28713 Z= 0.115 Angle : 0.631 15.771 38879 Z= 0.332 Chirality : 0.045 0.342 4333 Planarity : 0.004 0.088 4936 Dihedral : 6.361 39.848 3836 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.98 % Favored : 90.80 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.14), residues: 3509 helix: -0.03 (0.15), residues: 1179 sheet: -1.85 (0.22), residues: 571 loop : -2.59 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 96 HIS 0.009 0.001 HIS B 703 PHE 0.041 0.001 PHE D 144 TYR 0.047 0.001 TYR M 33 ARG 0.005 0.000 ARG H 99 Details of bonding type rmsd hydrogen bonds : bond 0.03342 ( 1053) hydrogen bonds : angle 5.75139 ( 2961) SS BOND : bond 0.00200 ( 14) SS BOND : angle 1.70227 ( 28) covalent geometry : bond 0.00242 (28699) covalent geometry : angle 0.62962 (38851) *********************** 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 163 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 3.212 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: 0.9655 (mmm) cc_final: 0.9217 (mmm) REVERT: A 375 MET cc_start: 0.8811 (tpt) cc_final: 0.7993 (mmm) REVERT: A 415 MET cc_start: 0.8094 (tpp) cc_final: 0.7727 (tpp) REVERT: A 436 MET cc_start: 0.9554 (mmp) cc_final: 0.9353 (mmp) REVERT: A 457 CYS cc_start: 0.9367 (m) cc_final: 0.9167 (m) REVERT: A 523 MET cc_start: 0.9618 (mmm) cc_final: 0.9190 (mtp) REVERT: A 576 MET cc_start: 0.9205 (mtp) cc_final: 0.8566 (tmm) REVERT: A 839 MET cc_start: 0.7766 (ptp) cc_final: 0.7408 (mpp) REVERT: B 132 MET cc_start: 0.8936 (ppp) cc_final: 0.8483 (ppp) REVERT: B 497 MET cc_start: 0.9328 (mtm) cc_final: 0.9121 (mpp) REVERT: B 654 MET cc_start: 0.9531 (mmp) cc_final: 0.9089 (mmp) REVERT: C 261 MET cc_start: 0.9670 (mmm) cc_final: 0.9226 (mmm) REVERT: C 375 MET cc_start: 0.8939 (tpt) cc_final: 0.8248 (mmm) REVERT: C 436 MET cc_start: 0.9560 (mmp) cc_final: 0.9348 (mmp) REVERT: C 523 MET cc_start: 0.9638 (mmm) cc_final: 0.9076 (mtp) REVERT: C 576 MET cc_start: 0.9236 (mtp) cc_final: 0.8561 (tmm) REVERT: C 834 MET cc_start: 0.9037 (mpp) cc_final: 0.8659 (mpp) REVERT: C 839 MET cc_start: 0.7884 (ptp) cc_final: 0.7593 (mpp) REVERT: D 132 MET cc_start: 0.8869 (ppp) cc_final: 0.8364 (ppp) REVERT: D 497 MET cc_start: 0.9333 (mtm) cc_final: 0.9133 (mpp) REVERT: D 654 MET cc_start: 0.9528 (mmp) cc_final: 0.8942 (mtp) REVERT: H 83 MET cc_start: 0.7424 (tpt) cc_final: 0.7056 (tpp) REVERT: M 106 MET cc_start: 0.7766 (mmp) cc_final: 0.7535 (mmp) REVERT: N 41 GLN cc_start: 0.8464 (pt0) cc_final: 0.8184 (pm20) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.3835 time to fit residues: 103.4867 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 : 3.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 344 optimal weight: 30.0000 chunk 36 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 304 optimal weight: 10.0000 chunk 326 optimal weight: 0.2980 chunk 165 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 157 optimal weight: 20.0000 chunk 15 optimal weight: 0.0980 chunk 196 optimal weight: 7.9990 chunk 156 optimal weight: 10.0000 overall best weight: 4.4786 ------------------------------------------------------------------------------- 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 ** B 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 802 HIS ** 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 = 0.2923 r_free = 0.2923 target = 0.027434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.022196 restraints weight = 493356.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.022824 restraints weight = 306908.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.023264 restraints weight = 213267.813| |-----------------------------------------------------------------------------| r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2869 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= 0.170 Angle : 0.646 12.237 38879 Z= 0.344 Chirality : 0.044 0.203 4333 Planarity : 0.004 0.083 4936 Dihedral : 6.318 39.479 3836 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.80 % Favored : 90.03 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.14), residues: 3509 helix: 0.23 (0.15), residues: 1180 sheet: -1.83 (0.21), residues: 571 loop : -2.53 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 402 HIS 0.007 0.001 HIS D 703 PHE 0.026 0.001 PHE B 563 TYR 0.037 0.001 TYR M 33 ARG 0.003 0.000 ARG H 67 Details of bonding type rmsd hydrogen bonds : bond 0.03365 ( 1053) hydrogen bonds : angle 5.69959 ( 2961) SS BOND : bond 0.00249 ( 14) SS BOND : angle 2.23536 ( 28) covalent geometry : bond 0.00347 (28699) covalent geometry : angle 0.64338 (38851) *********************** 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 : 3.292 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: 0.9700 (mmm) cc_final: 0.9255 (mmm) REVERT: A 375 MET cc_start: 0.9169 (tpt) cc_final: 0.8545 (mmm) REVERT: A 415 MET cc_start: 0.8058 (tpp) cc_final: 0.7679 (tpp) REVERT: A 523 MET cc_start: 0.9816 (mmm) cc_final: 0.8944 (mtp) REVERT: A 576 MET cc_start: 0.9200 (mtp) cc_final: 0.8494 (tmm) REVERT: A 834 MET cc_start: 0.9001 (mpp) cc_final: 0.8622 (mpp) REVERT: A 839 MET cc_start: 0.7946 (ptp) cc_final: 0.7593 (mpp) REVERT: B 132 MET cc_start: 0.8900 (ppp) cc_final: 0.8456 (ppp) REVERT: B 307 MET cc_start: 0.8641 (ppp) cc_final: 0.8396 (ppp) REVERT: B 497 MET cc_start: 0.9339 (mtm) cc_final: 0.9133 (mpp) REVERT: B 562 MET cc_start: 0.9713 (mpp) cc_final: 0.9214 (mmt) REVERT: B 565 MET cc_start: 0.9771 (mtm) cc_final: 0.9265 (mtm) REVERT: B 654 MET cc_start: 0.9528 (mmp) cc_final: 0.9074 (mmm) REVERT: C 261 MET cc_start: 0.9709 (mmm) cc_final: 0.9332 (mmm) REVERT: C 375 MET cc_start: 0.9191 (tpt) cc_final: 0.8606 (mmm) REVERT: C 523 MET cc_start: 0.9830 (mmm) cc_final: 0.8987 (mtp) REVERT: C 576 MET cc_start: 0.9150 (mtp) cc_final: 0.8421 (tmm) REVERT: C 834 MET cc_start: 0.9024 (mpp) cc_final: 0.8600 (mpp) REVERT: C 839 MET cc_start: 0.7983 (ptp) cc_final: 0.7646 (mpp) REVERT: D 132 MET cc_start: 0.8930 (ppp) cc_final: 0.8488 (ppp) REVERT: D 565 MET cc_start: 0.9737 (mtm) cc_final: 0.9284 (mtm) REVERT: D 654 MET cc_start: 0.9526 (mmp) cc_final: 0.9081 (mmm) REVERT: H 83 MET cc_start: 0.7278 (tpt) cc_final: 0.6900 (tpp) REVERT: M 106 MET cc_start: 0.7604 (mmp) cc_final: 0.7365 (mmp) REVERT: N 41 GLN cc_start: 0.8583 (pt0) cc_final: 0.8195 (pm20) REVERT: N 84 GLU cc_start: 0.9112 (pp20) cc_final: 0.8838 (mp0) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.4031 time to fit residues: 107.8123 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 : 3.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 102 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 225 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 229 optimal weight: 0.3980 chunk 54 optimal weight: 20.0000 chunk 332 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 341 optimal weight: 7.9990 chunk 300 optimal weight: 0.3980 chunk 134 optimal weight: 7.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- 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** C 378 GLN C 748 HIS ** 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 = 0.2929 r_free = 0.2929 target = 0.027551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.022356 restraints weight = 494352.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.022999 restraints weight = 301744.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.023462 restraints weight = 211329.861| |-----------------------------------------------------------------------------| r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3102 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= 0.143 Angle : 0.617 8.506 38879 Z= 0.329 Chirality : 0.044 0.236 4333 Planarity : 0.004 0.082 4936 Dihedral : 6.227 38.495 3836 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.32 % Favored : 89.51 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.14), residues: 3509 helix: 0.37 (0.15), residues: 1181 sheet: -1.78 (0.21), residues: 566 loop : -2.52 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 402 HIS 0.007 0.001 HIS D 703 PHE 0.034 0.001 PHE B 525 TYR 0.035 0.001 TYR M 33 ARG 0.003 0.000 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.03212 ( 1053) hydrogen bonds : angle 5.55137 ( 2961) SS BOND : bond 0.00278 ( 14) SS BOND : angle 2.19886 ( 28) covalent geometry : bond 0.00299 (28699) covalent geometry : angle 0.61486 (38851) *********************** 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 : 3.525 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 155 MET cc_start: 0.8619 (mmp) cc_final: 0.7953 (tpt) REVERT: A 261 MET cc_start: 0.9690 (mmm) cc_final: 0.9336 (mmm) REVERT: A 415 MET cc_start: 0.8018 (tpp) cc_final: 0.7588 (tpp) REVERT: A 523 MET cc_start: 0.9804 (mmm) cc_final: 0.9006 (mtp) REVERT: A 576 MET cc_start: 0.9105 (mtp) cc_final: 0.8476 (tmm) REVERT: A 655 MET cc_start: 0.8576 (tpp) cc_final: 0.8367 (tpp) REVERT: A 839 MET cc_start: 0.8003 (ptp) cc_final: 0.7787 (ptp) REVERT: B 565 MET cc_start: 0.9701 (mtm) cc_final: 0.9360 (mtt) REVERT: B 654 MET cc_start: 0.9540 (mmp) cc_final: 0.9108 (mmm) REVERT: C 155 MET cc_start: 0.8677 (mmp) cc_final: 0.8028 (tpt) REVERT: C 261 MET cc_start: 0.9699 (mmm) cc_final: 0.9325 (mmm) REVERT: C 523 MET cc_start: 0.9788 (mmm) cc_final: 0.9083 (mtp) REVERT: C 576 MET cc_start: 0.9177 (mtp) cc_final: 0.8481 (tmm) REVERT: C 834 MET cc_start: 0.9063 (mpp) cc_final: 0.8720 (mpp) REVERT: C 839 MET cc_start: 0.8048 (ptp) cc_final: 0.7663 (mpp) REVERT: D 132 MET cc_start: 0.9018 (ppp) cc_final: 0.8570 (ppp) REVERT: D 307 MET cc_start: 0.8392 (ppp) cc_final: 0.8147 (ppp) REVERT: D 654 MET cc_start: 0.9549 (mmp) cc_final: 0.9085 (mmm) REVERT: N 41 GLN cc_start: 0.8637 (pt0) cc_final: 0.8216 (pm20) REVERT: N 84 GLU cc_start: 0.8989 (pp20) cc_final: 0.8764 (mp0) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.4275 time to fit residues: 113.5314 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 : 3.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 327 optimal weight: 20.0000 chunk 317 optimal weight: 9.9990 chunk 301 optimal weight: 0.0980 chunk 23 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 chunk 232 optimal weight: 20.0000 chunk 67 optimal weight: 8.9990 chunk 226 optimal weight: 10.0000 chunk 340 optimal weight: 30.0000 chunk 82 optimal weight: 0.8980 chunk 250 optimal weight: 0.5980 overall best weight: 3.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 694 ASN ** 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 = 0.2920 r_free = 0.2920 target = 0.027387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.022188 restraints weight = 492112.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.022823 restraints weight = 304672.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.023270 restraints weight = 213184.624| |-----------------------------------------------------------------------------| r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28713 Z= 0.153 Angle : 0.629 8.483 38879 Z= 0.336 Chirality : 0.044 0.243 4333 Planarity : 0.004 0.083 4936 Dihedral : 6.210 40.191 3836 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.06 % Favored : 89.71 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.14), residues: 3509 helix: 0.33 (0.15), residues: 1208 sheet: -1.84 (0.21), residues: 579 loop : -2.55 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 610 HIS 0.008 0.001 HIS C 748 PHE 0.043 0.002 PHE D 144 TYR 0.041 0.001 TYR H 33 ARG 0.007 0.000 ARG L 65 Details of bonding type rmsd hydrogen bonds : bond 0.03234 ( 1053) hydrogen bonds : angle 5.50567 ( 2961) SS BOND : bond 0.00276 ( 14) SS BOND : angle 2.48532 ( 28) covalent geometry : bond 0.00318 (28699) covalent geometry : angle 0.62577 (38851) *********************** 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 155 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 3.453 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: A 155 MET cc_start: 0.8669 (mmp) cc_final: 0.8189 (tpt) REVERT: A 261 MET cc_start: 0.9713 (mmm) cc_final: 0.9291 (mmm) REVERT: A 415 MET cc_start: 0.8107 (tpp) cc_final: 0.7660 (tpp) REVERT: A 523 MET cc_start: 0.9785 (mmm) cc_final: 0.9183 (mtp) REVERT: A 576 MET cc_start: 0.9127 (mtp) cc_final: 0.8498 (tmm) REVERT: B 654 MET cc_start: 0.9555 (mmp) cc_final: 0.9200 (mmm) REVERT: B 809 MET cc_start: 0.8960 (mmt) cc_final: 0.8501 (mmm) REVERT: C 155 MET cc_start: 0.8721 (mmp) cc_final: 0.8164 (tpt) REVERT: C 261 MET cc_start: 0.9692 (mmm) cc_final: 0.9249 (mmm) REVERT: C 523 MET cc_start: 0.9785 (mmm) cc_final: 0.9170 (mtp) REVERT: C 576 MET cc_start: 0.9158 (mtp) cc_final: 0.8508 (tmm) REVERT: D 132 MET cc_start: 0.9074 (ppp) cc_final: 0.8606 (ppp) REVERT: D 307 MET cc_start: 0.8365 (ppp) cc_final: 0.8117 (ppp) REVERT: D 565 MET cc_start: 0.9758 (mtm) cc_final: 0.9423 (mtt) REVERT: D 654 MET cc_start: 0.9565 (mmp) cc_final: 0.9216 (mmm) REVERT: M 106 MET cc_start: 0.7618 (mmp) cc_final: 0.6896 (mmp) REVERT: N 84 GLU cc_start: 0.9025 (pp20) cc_final: 0.8756 (mp0) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.4341 time to fit residues: 113.6251 Evaluate side-chains 141 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 3.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 276 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 9 optimal weight: 0.3980 chunk 98 optimal weight: 2.9990 chunk 259 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 245 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 257 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.028043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.022821 restraints weight = 487902.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.023480 restraints weight = 296484.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.023944 restraints weight = 205169.474| |-----------------------------------------------------------------------------| r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 28713 Z= 0.109 Angle : 0.608 9.465 38879 Z= 0.321 Chirality : 0.044 0.229 4333 Planarity : 0.004 0.083 4936 Dihedral : 6.063 40.656 3836 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.60 % Favored : 90.23 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.14), residues: 3509 helix: 0.45 (0.15), residues: 1207 sheet: -1.76 (0.22), residues: 550 loop : -2.52 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP D 166 HIS 0.007 0.001 HIS D 703 PHE 0.028 0.001 PHE D 525 TYR 0.053 0.001 TYR M 33 ARG 0.005 0.000 ARG H 99 Details of bonding type rmsd hydrogen bonds : bond 0.03032 ( 1053) hydrogen bonds : angle 5.32503 ( 2961) SS BOND : bond 0.00317 ( 14) SS BOND : angle 2.65033 ( 28) covalent geometry : bond 0.00237 (28699) covalent geometry : angle 0.60392 (38851) *********************** 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 157 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 3.266 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 155 MET cc_start: 0.8805 (mmp) cc_final: 0.8380 (tpt) REVERT: A 261 MET cc_start: 0.9713 (mmm) cc_final: 0.9317 (mmm) REVERT: A 415 MET cc_start: 0.8336 (tpp) cc_final: 0.7937 (tpp) REVERT: A 523 MET cc_start: 0.9790 (mmm) cc_final: 0.9215 (mtp) REVERT: A 576 MET cc_start: 0.9110 (mtp) cc_final: 0.8455 (tmm) REVERT: A 839 MET cc_start: 0.8137 (ptp) cc_final: 0.7795 (mpp) REVERT: B 654 MET cc_start: 0.9531 (mmp) cc_final: 0.9159 (mmm) REVERT: B 809 MET cc_start: 0.8896 (mmt) cc_final: 0.8459 (mmm) REVERT: C 125 MET cc_start: 0.9493 (mmp) cc_final: 0.9271 (mmm) REVERT: C 155 MET cc_start: 0.8827 (mmp) cc_final: 0.8366 (tpt) REVERT: C 261 MET cc_start: 0.9717 (mmm) cc_final: 0.9245 (mmm) REVERT: C 523 MET cc_start: 0.9792 (mmm) cc_final: 0.9197 (mtp) REVERT: C 576 MET cc_start: 0.9140 (mtp) cc_final: 0.8468 (tmm) REVERT: C 839 MET cc_start: 0.8178 (ptp) cc_final: 0.7844 (mpp) REVERT: D 132 MET cc_start: 0.9109 (ppp) cc_final: 0.8535 (ppp) REVERT: D 307 MET cc_start: 0.8387 (ppp) cc_final: 0.8120 (ppp) REVERT: D 654 MET cc_start: 0.9561 (mmp) cc_final: 0.9197 (mmm) REVERT: M 106 MET cc_start: 0.7771 (mmp) cc_final: 0.7434 (mmp) REVERT: N 84 GLU cc_start: 0.8962 (pp20) cc_final: 0.8728 (mp0) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.3789 time to fit residues: 99.7129 Evaluate side-chains 143 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 4.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 17 optimal weight: 9.9990 chunk 87 optimal weight: 20.0000 chunk 246 optimal weight: 5.9990 chunk 188 optimal weight: 30.0000 chunk 145 optimal weight: 3.9990 chunk 273 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 304 optimal weight: 0.6980 chunk 331 optimal weight: 0.4980 chunk 193 optimal weight: 3.9990 chunk 227 optimal weight: 0.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.028199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.022990 restraints weight = 484695.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.023648 restraints weight = 295562.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.024109 restraints weight = 204382.948| |-----------------------------------------------------------------------------| r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 28713 Z= 0.108 Angle : 0.611 9.112 38879 Z= 0.322 Chirality : 0.044 0.330 4333 Planarity : 0.004 0.084 4936 Dihedral : 5.945 38.760 3836 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.52 % Favored : 90.31 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.44 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.14), residues: 3509 helix: 0.48 (0.15), residues: 1210 sheet: -1.71 (0.21), residues: 566 loop : -2.52 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP B 166 HIS 0.006 0.001 HIS D 703 PHE 0.040 0.001 PHE B 144 TYR 0.045 0.001 TYR M 33 ARG 0.004 0.000 ARG H 99 Details of bonding type rmsd hydrogen bonds : bond 0.02960 ( 1053) hydrogen bonds : angle 5.25650 ( 2961) SS BOND : bond 0.00329 ( 14) SS BOND : angle 2.75819 ( 28) covalent geometry : bond 0.00231 (28699) covalent geometry : angle 0.60691 (38851) *********************** 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 157 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 3.382 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 155 MET cc_start: 0.8816 (mmp) cc_final: 0.8381 (tpt) REVERT: A 261 MET cc_start: 0.9718 (mmm) cc_final: 0.9232 (mmm) REVERT: A 375 MET cc_start: 0.8721 (tpp) cc_final: 0.8399 (tpp) REVERT: A 415 MET cc_start: 0.8365 (tpp) cc_final: 0.7973 (tpp) REVERT: A 523 MET cc_start: 0.9790 (mmm) cc_final: 0.9240 (mtp) REVERT: A 576 MET cc_start: 0.9154 (mtp) cc_final: 0.8437 (tmm) REVERT: A 839 MET cc_start: 0.8113 (ptp) cc_final: 0.7798 (mpp) REVERT: B 41 LEU cc_start: 0.9748 (mp) cc_final: 0.9527 (tt) REVERT: B 654 MET cc_start: 0.9515 (mmp) cc_final: 0.9186 (mmp) REVERT: B 809 MET cc_start: 0.8894 (mmt) cc_final: 0.8525 (mmm) REVERT: C 125 MET cc_start: 0.9490 (mmp) cc_final: 0.9287 (mmm) REVERT: C 155 MET cc_start: 0.8876 (mmp) cc_final: 0.8403 (tpt) REVERT: C 261 MET cc_start: 0.9717 (mmm) cc_final: 0.9241 (mmm) REVERT: C 375 MET cc_start: 0.8719 (tpp) cc_final: 0.8395 (tpp) REVERT: C 523 MET cc_start: 0.9791 (mmm) cc_final: 0.9225 (mtp) REVERT: C 576 MET cc_start: 0.9130 (mtp) cc_final: 0.8437 (tmm) REVERT: C 839 MET cc_start: 0.8161 (ptp) cc_final: 0.7861 (mpp) REVERT: D 132 MET cc_start: 0.9114 (ppp) cc_final: 0.8521 (ppp) REVERT: D 307 MET cc_start: 0.8280 (ppp) cc_final: 0.8014 (ppp) REVERT: D 654 MET cc_start: 0.9558 (mmp) cc_final: 0.9200 (mmm) REVERT: M 106 MET cc_start: 0.7875 (mmp) cc_final: 0.7532 (mmp) REVERT: N 84 GLU cc_start: 0.8953 (pp20) cc_final: 0.8723 (mp0) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.3856 time to fit residues: 102.4130 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 : 3.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 159 optimal weight: 0.9980 chunk 136 optimal weight: 0.0050 chunk 257 optimal weight: 8.9990 chunk 141 optimal weight: 5.9990 chunk 285 optimal weight: 9.9990 chunk 287 optimal weight: 6.9990 chunk 185 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 183 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 overall best weight: 2.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 323 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.027861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.022629 restraints weight = 488041.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.023275 restraints weight = 299847.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.023729 restraints weight = 208967.336| |-----------------------------------------------------------------------------| r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28713 Z= 0.127 Angle : 0.626 12.489 38879 Z= 0.330 Chirality : 0.044 0.294 4333 Planarity : 0.004 0.083 4936 Dihedral : 5.923 37.612 3836 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.06 % Favored : 89.77 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.14), residues: 3509 helix: 0.53 (0.15), residues: 1211 sheet: -1.75 (0.21), residues: 573 loop : -2.46 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 166 HIS 0.006 0.001 HIS D 703 PHE 0.024 0.001 PHE D 525 TYR 0.043 0.001 TYR M 33 ARG 0.006 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.03002 ( 1053) hydrogen bonds : angle 5.28498 ( 2961) SS BOND : bond 0.00287 ( 14) SS BOND : angle 2.93602 ( 28) covalent geometry : bond 0.00267 (28699) covalent geometry : angle 0.62152 (38851) ********************** 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 152 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 3.678 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 155 MET cc_start: 0.8805 (mmp) cc_final: 0.8387 (tpt) REVERT: A 261 MET cc_start: 0.9698 (mmm) cc_final: 0.9274 (mmm) REVERT: A 415 MET cc_start: 0.8369 (tpp) cc_final: 0.7931 (tpp) REVERT: A 523 MET cc_start: 0.9789 (mmm) cc_final: 0.9257 (mtp) REVERT: A 576 MET cc_start: 0.9112 (mtp) cc_final: 0.8444 (tmm) REVERT: A 839 MET cc_start: 0.8129 (ptp) cc_final: 0.7816 (mpp) REVERT: B 41 LEU cc_start: 0.9755 (mp) cc_final: 0.9512 (tt) REVERT: B 565 MET cc_start: 0.9761 (mtm) cc_final: 0.9482 (mtt) REVERT: B 654 MET cc_start: 0.9514 (mmp) cc_final: 0.9171 (mmp) REVERT: B 809 MET cc_start: 0.8943 (mmt) cc_final: 0.8570 (mmm) REVERT: C 155 MET cc_start: 0.8827 (mmp) cc_final: 0.8349 (tpt) REVERT: C 261 MET cc_start: 0.9686 (mmm) cc_final: 0.9287 (mmm) REVERT: C 523 MET cc_start: 0.9787 (mmm) cc_final: 0.9240 (mtp) REVERT: C 576 MET cc_start: 0.9141 (mtp) cc_final: 0.8458 (tmm) REVERT: C 839 MET cc_start: 0.8274 (ptp) cc_final: 0.7996 (mpp) REVERT: D 132 MET cc_start: 0.9115 (ppp) cc_final: 0.8533 (ppp) REVERT: D 307 MET cc_start: 0.8317 (ppp) cc_final: 0.8045 (ppp) REVERT: D 654 MET cc_start: 0.9561 (mmp) cc_final: 0.9271 (mmp) REVERT: M 106 MET cc_start: 0.7942 (mmp) cc_final: 0.7620 (mmp) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.3855 time to fit residues: 98.7867 Evaluate side-chains 138 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 3.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 267 optimal weight: 10.0000 chunk 197 optimal weight: 5.9990 chunk 281 optimal weight: 0.9990 chunk 195 optimal weight: 7.9990 chunk 164 optimal weight: 6.9990 chunk 213 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 311 optimal weight: 20.0000 chunk 310 optimal weight: 50.0000 chunk 8 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2932 r_free = 0.2932 target = 0.027670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.022440 restraints weight = 491387.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.023075 restraints weight = 303133.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.023532 restraints weight = 210384.619| |-----------------------------------------------------------------------------| r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28713 Z= 0.133 Angle : 0.622 10.031 38879 Z= 0.329 Chirality : 0.044 0.273 4333 Planarity : 0.004 0.084 4936 Dihedral : 5.920 37.164 3836 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.77 % Favored : 90.05 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.97 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.14), residues: 3509 helix: 0.57 (0.15), residues: 1214 sheet: -1.80 (0.20), residues: 591 loop : -2.44 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 166 HIS 0.006 0.001 HIS A 748 PHE 0.025 0.001 PHE D 525 TYR 0.041 0.001 TYR M 33 ARG 0.005 0.000 ARG B 187 Details of bonding type rmsd hydrogen bonds : bond 0.03056 ( 1053) hydrogen bonds : angle 5.29544 ( 2961) SS BOND : bond 0.00232 ( 14) SS BOND : angle 2.79825 ( 28) covalent geometry : bond 0.00279 (28699) covalent geometry : angle 0.61807 (38851) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7438.59 seconds wall clock time: 130 minutes 48.02 seconds (7848.02 seconds total)