Starting phenix.real_space_refine on Thu Mar 5 13:46:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6whs_21674/03_2026/6whs_21674.cif Found real_map, /net/cci-nas-00/data/ceres_data/6whs_21674/03_2026/6whs_21674.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6whs_21674/03_2026/6whs_21674.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6whs_21674/03_2026/6whs_21674.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6whs_21674/03_2026/6whs_21674.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6whs_21674/03_2026/6whs_21674.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.725 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 298 atoms to isotropic. 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 110 5.16 5 C 14694 2.51 5 N 3730 2.21 5 O 4332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22866 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 5705 Classifications: {'peptide': 799} Incomplete info: {'truncation_to_alanine': 144} Link IDs: {'PTRANS': 35, 'TRANS': 763} Chain breaks: 3 Unresolved non-hydrogen bonds: 620 Unresolved non-hydrogen angles: 733 Unresolved non-hydrogen dihedrals: 534 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 30, 'HIS:plan': 6, 'GLU:plan': 22, 'GLN:plan1': 7, 'PHE:plan': 4, 'ASN:plan1': 8, 'ASP:plan': 14, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 395 Chain: "B" Number of atoms: 5644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 5644 Classifications: {'peptide': 787} Incomplete info: {'truncation_to_alanine': 137} Link IDs: {'PTRANS': 27, 'TRANS': 759} Chain breaks: 2 Unresolved non-hydrogen bonds: 594 Unresolved non-hydrogen angles: 713 Unresolved non-hydrogen dihedrals: 524 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 14, 'GLU:plan': 32, 'HIS:plan': 5, 'ASN:plan1': 3, 'ARG:plan': 10, 'GLN:plan1': 10, 'TYR:plan': 8, 'TRP:plan': 1, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 383 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: C, D, F Time building chain proxies: 8.79, per 1000 atoms: 0.38 Number of scatterers: 22866 At special positions: 0 Unit cell: (138.37, 154.81, 179.47, 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 110 16.00 O 4332 8.00 N 3730 7.00 C 14694 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=2.06 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.02 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 B 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 329 " distance=2.06 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.02 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 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1001 " - " ASN A 224 " " NAG A1002 " - " ASN A 297 " " NAG B 903 " - " ASN B 491 " " NAG B 904 " - " ASN B 341 " " NAG C1001 " - " ASN C 224 " " NAG C1002 " - " ASN C 297 " " NAG D 903 " - " ASN D 491 " " NAG D 904 " - " ASN D 341 " " NAG E 1 " - " ASN B 688 " " NAG F 1 " - " ASN D 688 " Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 1.0 seconds 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5924 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 38 sheets defined 43.3% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 70 through 86 removed outlier: 3.717A pdb=" N MET A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N CYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 113 removed outlier: 3.562A pdb=" N TYR A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.793A pdb=" N TYR A 128 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 150 removed outlier: 3.909A pdb=" N GLN A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 158 removed outlier: 3.889A pdb=" N MET A 154 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 186 Processing helix chain 'A' and resid 225 through 235 removed outlier: 3.979A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 260 Processing helix chain 'A' and resid 276 through 283 removed outlier: 3.528A pdb=" N ALA A 279 " --> pdb=" O SER A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 317 removed outlier: 3.582A pdb=" N HIS A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU A 315 " --> pdb=" O GLN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 480 through 492 Processing helix chain 'A' and resid 520 through 529 removed outlier: 3.845A pdb=" N GLY A 524 " --> pdb=" O ASN A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 580 through 604 removed outlier: 3.530A pdb=" N TRP A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 removed outlier: 3.905A pdb=" N TRP A 629 " --> pdb=" O SER A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 676 removed outlier: 3.813A pdb=" N LEU A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N MET A 655 " --> pdb=" O ARG A 651 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 694 Processing helix chain 'A' and resid 708 through 717 removed outlier: 3.782A pdb=" N GLN A 717 " --> pdb=" O TYR A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 729 removed outlier: 3.987A pdb=" N LYS A 729 " --> pdb=" O ARG A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 744 removed outlier: 3.592A pdb=" N ASP A 744 " --> pdb=" O GLN A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 764 removed outlier: 4.764A pdb=" N PHE A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 803 Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 830 through 862 removed outlier: 4.053A pdb=" N MET A 834 " --> pdb=" O THR A 830 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLY A 836 " --> pdb=" O GLU A 832 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL A 837 " --> pdb=" O ASN A 833 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU A 840 " --> pdb=" O GLY A 836 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 849 " --> pdb=" O ILE A 845 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE A 850 " --> pdb=" O VAL A 846 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU A 851 " --> pdb=" O ALA A 847 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG A 860 " --> pdb=" O ILE A 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 77 through 92 Processing helix chain 'B' and resid 106 through 119 Processing helix chain 'B' and resid 127 through 132 removed outlier: 3.761A pdb=" N SER B 130 " --> pdb=" O HIS B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 removed outlier: 3.877A pdb=" N GLN B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 163 " --> pdb=" O ASN B 159 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 191 removed outlier: 3.575A pdb=" N PHE B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 235 through 246 removed outlier: 4.417A pdb=" N TYR B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 289 through 311 removed outlier: 3.937A pdb=" N VAL B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 340 removed outlier: 4.045A pdb=" N ILE B 340 " --> pdb=" O ASN B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 472 Processing helix chain 'B' and resid 495 through 503 Processing helix chain 'B' and resid 516 through 521 removed outlier: 3.610A pdb=" N SER B 520 " --> pdb=" O ASN B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 580 removed outlier: 3.612A pdb=" N MET B 561 " --> pdb=" O CYS B 557 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA B 571 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR B 579 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE B 580 " --> pdb=" O VAL B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 615 removed outlier: 3.982A pdb=" N PHE B 614 " --> pdb=" O TRP B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 656 removed outlier: 3.667A pdb=" N SER B 633 " --> pdb=" O LYS B 629 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 634 " --> pdb=" O ILE B 630 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TRP B 635 " --> pdb=" O MET B 631 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA B 644 " --> pdb=" O VAL B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 674 through 677 Processing helix chain 'B' and resid 689 through 696 Processing helix chain 'B' and resid 699 through 707 Processing helix chain 'B' and resid 714 through 723 Processing helix chain 'B' and resid 733 through 741 Processing helix chain 'B' and resid 771 through 786 removed outlier: 3.845A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA B 779 " --> pdb=" O GLN B 775 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 783 " --> pdb=" O ALA B 779 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE B 784 " --> pdb=" O ILE B 780 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP B 786 " --> pdb=" O GLN B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 Processing helix chain 'B' and resid 814 through 844 removed outlier: 4.469A pdb=" N MET B 818 " --> pdb=" O ASP B 814 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA B 819 " --> pdb=" O ILE B 815 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY B 820 " --> pdb=" O ASP B 816 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL B 821 " --> pdb=" O ASN B 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 50 Processing helix chain 'C' and resid 70 through 86 removed outlier: 3.718A pdb=" N MET C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N CYS C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 113 removed outlier: 3.561A pdb=" N TYR C 109 " --> pdb=" O THR C 105 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA C 111 " --> pdb=" O VAL C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.793A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 150 removed outlier: 3.910A pdb=" N GLN C 147 " --> pdb=" O PRO C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 158 removed outlier: 3.889A pdb=" N MET C 154 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 225 through 235 removed outlier: 3.979A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 260 Processing helix chain 'C' and resid 276 through 283 removed outlier: 3.527A pdb=" N ALA C 279 " --> pdb=" O SER C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 317 removed outlier: 3.582A pdb=" N HIS C 301 " --> pdb=" O ASN C 297 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU C 315 " --> pdb=" O GLN C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 347 Processing helix chain 'C' and resid 480 through 492 Processing helix chain 'C' and resid 520 through 529 removed outlier: 3.845A pdb=" N GLY C 524 " --> pdb=" O ASN C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 580 through 604 removed outlier: 3.530A pdb=" N TRP C 584 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS C 592 " --> pdb=" O GLY C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 637 removed outlier: 3.905A pdb=" N TRP C 629 " --> pdb=" O SER C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 676 removed outlier: 3.813A pdb=" N LEU C 653 " --> pdb=" O SER C 649 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N MET C 655 " --> pdb=" O ARG C 651 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 694 Processing helix chain 'C' and resid 708 through 717 removed outlier: 3.782A pdb=" N GLN C 717 " --> pdb=" O TYR C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 729 removed outlier: 3.985A pdb=" N LYS C 729 " --> pdb=" O ARG C 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 744 removed outlier: 3.593A pdb=" N ASP C 744 " --> pdb=" O GLN C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 764 removed outlier: 4.764A pdb=" N PHE C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 803 Processing helix chain 'C' and resid 804 through 814 Processing helix chain 'C' and resid 830 through 862 removed outlier: 4.052A pdb=" N MET C 834 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLY C 836 " --> pdb=" O GLU C 832 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL C 837 " --> pdb=" O ASN C 833 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU C 840 " --> pdb=" O GLY C 836 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE C 849 " --> pdb=" O ILE C 845 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE C 850 " --> pdb=" O VAL C 846 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU C 851 " --> pdb=" O ALA C 847 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG C 860 " --> pdb=" O ILE C 856 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 54 Processing helix chain 'D' and resid 77 through 92 Processing helix chain 'D' and resid 106 through 119 Processing helix chain 'D' and resid 127 through 132 removed outlier: 3.761A pdb=" N SER D 130 " --> pdb=" O HIS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 164 removed outlier: 3.877A pdb=" N GLN D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU D 163 " --> pdb=" O ASN D 159 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR D 164 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 191 removed outlier: 3.577A pdb=" N PHE D 182 " --> pdb=" O GLY D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 235 through 246 removed outlier: 4.417A pdb=" N TYR D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 283 through 288 Processing helix chain 'D' and resid 289 through 311 removed outlier: 3.936A pdb=" N VAL D 293 " --> pdb=" O LEU D 289 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU D 310 " --> pdb=" O ASP D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 340 removed outlier: 4.045A pdb=" N ILE D 340 " --> pdb=" O ASN D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 472 Processing helix chain 'D' and resid 495 through 503 Processing helix chain 'D' and resid 516 through 521 removed outlier: 3.610A pdb=" N SER D 520 " --> pdb=" O ASN D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 580 removed outlier: 3.611A pdb=" N MET D 561 " --> pdb=" O CYS D 557 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA D 571 " --> pdb=" O LEU D 567 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR D 579 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE D 580 " --> pdb=" O VAL D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 615 removed outlier: 3.982A pdb=" N PHE D 614 " --> pdb=" O TRP D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 656 removed outlier: 3.666A pdb=" N SER D 633 " --> pdb=" O LYS D 629 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL D 634 " --> pdb=" O ILE D 630 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TRP D 635 " --> pdb=" O MET D 631 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA D 644 " --> pdb=" O VAL D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 674 through 677 Processing helix chain 'D' and resid 689 through 696 Processing helix chain 'D' and resid 699 through 707 Processing helix chain 'D' and resid 714 through 723 Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 771 through 786 removed outlier: 3.845A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA D 779 " --> pdb=" O GLN D 775 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU D 783 " --> pdb=" O ALA D 779 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE D 784 " --> pdb=" O ILE D 780 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP D 786 " --> pdb=" O GLN D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 797 Processing helix chain 'D' and resid 814 through 844 removed outlier: 4.470A pdb=" N MET D 818 " --> pdb=" O ASP D 814 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA D 819 " --> pdb=" O ILE D 815 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY D 820 " --> pdb=" O ASP D 816 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL D 821 " --> pdb=" O ASN D 817 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 65 removed outlier: 9.141A pdb=" N VAL A 87 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASN A 28 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA A 89 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N LEU A 119 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 215 through 218 removed outlier: 7.379A pdb=" N LEU A 165 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N PHE A 218 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL A 167 " --> pdb=" O PHE A 218 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER A 168 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 292 removed outlier: 5.935A pdb=" N ASN A 376 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N GLN A 384 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLN A 378 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N LEU A 382 " --> pdb=" O GLN A 378 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 360 through 361 removed outlier: 4.093A pdb=" N GLU A 360 " --> pdb=" O LYS A 368 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 418 through 423 removed outlier: 7.657A pdb=" N LEU A 419 " --> pdb=" O GLU A 496 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N HIS A 498 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ILE A 421 " --> pdb=" O HIS A 498 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 430 through 434 Processing sheet with id=AA7, first strand: chain 'A' and resid 508 through 511 removed outlier: 4.590A pdb=" N LYS A 516 " --> pdb=" O VAL A 511 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 549 through 550 Processing sheet with id=AA9, first strand: chain 'A' and resid 555 through 557 Processing sheet with id=AB1, first strand: chain 'A' and resid 750 through 753 Processing sheet with id=AB2, first strand: chain 'B' and resid 67 through 71 removed outlier: 3.511A pdb=" N GLU B 69 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLY B 36 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL B 97 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA B 38 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N PHE B 99 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE B 40 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 9.303A pdb=" N LEU B 124 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 198 through 199 removed outlier: 3.845A pdb=" N PHE B 169 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N LEU B 203 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 198 through 199 removed outlier: 3.845A pdb=" N PHE B 169 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 257 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N VAL B 258 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N TYR B 282 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU B 366 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ARG B 375 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 343 through 344 Processing sheet with id=AB6, first strand: chain 'B' and resid 405 through 409 removed outlier: 6.797A pdb=" N LEU B 406 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N TYR B 479 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE B 408 " --> pdb=" O TYR B 479 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU B 478 " --> pdb=" O PRO B 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AB8, first strand: chain 'B' and resid 508 through 509 Processing sheet with id=AB9, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC1, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.687A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N ASP B 732 " --> pdb=" O GLY B 684 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 59 through 65 removed outlier: 9.141A pdb=" N VAL C 87 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASN C 28 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA C 89 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 215 through 218 removed outlier: 7.379A pdb=" N LEU C 165 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N PHE C 218 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL C 167 " --> pdb=" O PHE C 218 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER C 168 " --> pdb=" O SER C 243 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 288 through 292 removed outlier: 5.935A pdb=" N ASN C 376 " --> pdb=" O GLN C 384 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N GLN C 384 " --> pdb=" O ASN C 376 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLN C 378 " --> pdb=" O LEU C 382 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LEU C 382 " --> pdb=" O GLN C 378 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 360 through 361 removed outlier: 4.093A pdb=" N GLU C 360 " --> pdb=" O LYS C 368 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 418 through 423 removed outlier: 7.657A pdb=" N LEU C 419 " --> pdb=" O GLU C 496 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N HIS C 498 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE C 421 " --> pdb=" O HIS C 498 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 430 through 434 Processing sheet with id=AC8, first strand: chain 'C' and resid 508 through 511 removed outlier: 4.590A pdb=" N LYS C 516 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 549 through 550 Processing sheet with id=AD1, first strand: chain 'C' and resid 555 through 557 Processing sheet with id=AD2, first strand: chain 'C' and resid 750 through 753 Processing sheet with id=AD3, first strand: chain 'D' and resid 67 through 71 removed outlier: 3.511A pdb=" N GLU D 69 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLY D 36 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL D 97 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA D 38 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N PHE D 99 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE D 40 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N LEU D 124 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 198 through 199 removed outlier: 3.845A pdb=" N PHE D 169 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N LEU D 203 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 198 through 199 removed outlier: 3.845A pdb=" N PHE D 169 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE D 257 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL D 258 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N TYR D 282 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU D 366 " --> pdb=" O ARG D 375 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ARG D 375 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 343 through 344 Processing sheet with id=AD7, first strand: chain 'D' and resid 405 through 409 removed outlier: 6.798A pdb=" N LEU D 406 " --> pdb=" O ASP D 477 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N TYR D 479 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE D 408 " --> pdb=" O TYR D 479 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU D 478 " --> pdb=" O PRO D 435 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AD9, first strand: chain 'D' and resid 508 through 509 Processing sheet with id=AE1, first strand: chain 'D' and resid 531 through 532 Processing sheet with id=AE2, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.688A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 8.966A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) 1038 hydrogen bonds defined for protein. 2946 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: 4.26 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7419 1.35 - 1.48: 6118 1.48 - 1.60: 9641 1.60 - 1.73: 0 1.73 - 1.86: 178 Bond restraints: 23356 Sorted by residual: bond pdb=" CA ARG D 696 " pdb=" C ARG D 696 " ideal model delta sigma weight residual 1.523 1.461 0.062 1.34e-02 5.57e+03 2.12e+01 bond pdb=" CA ARG B 696 " pdb=" C ARG B 696 " ideal model delta sigma weight residual 1.523 1.462 0.062 1.34e-02 5.57e+03 2.12e+01 bond pdb=" C1 NAG D 903 " pdb=" O5 NAG D 903 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C1 NAG B 903 " pdb=" O5 NAG B 903 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" CA LEU A 676 " pdb=" C LEU A 676 " ideal model delta sigma weight residual 1.523 1.479 0.044 1.80e-02 3.09e+03 6.05e+00 ... (remaining 23351 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 30919 2.28 - 4.56: 981 4.56 - 6.83: 89 6.83 - 9.11: 27 9.11 - 11.39: 6 Bond angle restraints: 32022 Sorted by residual: angle pdb=" N GLU C 682 " pdb=" CA GLU C 682 " pdb=" C GLU C 682 " ideal model delta sigma weight residual 111.71 118.78 -7.07 1.15e+00 7.56e-01 3.78e+01 angle pdb=" N GLU A 682 " pdb=" CA GLU A 682 " pdb=" C GLU A 682 " ideal model delta sigma weight residual 111.71 118.74 -7.03 1.15e+00 7.56e-01 3.73e+01 angle pdb=" C ILE C 688 " pdb=" CA ILE C 688 " pdb=" CB ILE C 688 " ideal model delta sigma weight residual 111.29 102.22 9.07 1.64e+00 3.72e-01 3.06e+01 angle pdb=" C ILE A 688 " pdb=" CA ILE A 688 " pdb=" CB ILE A 688 " ideal model delta sigma weight residual 111.29 102.31 8.98 1.64e+00 3.72e-01 3.00e+01 angle pdb=" CA LEU A 676 " pdb=" C LEU A 676 " pdb=" N VAL A 677 " ideal model delta sigma weight residual 118.27 126.46 -8.19 1.59e+00 3.96e-01 2.65e+01 ... (remaining 32017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.85: 13019 23.85 - 47.70: 677 47.70 - 71.55: 64 71.55 - 95.40: 18 95.40 - 119.25: 6 Dihedral angle restraints: 13784 sinusoidal: 4606 harmonic: 9178 Sorted by residual: dihedral pdb=" CA GLU C 682 " pdb=" C GLU C 682 " pdb=" N GLU C 683 " pdb=" CA GLU C 683 " ideal model delta harmonic sigma weight residual -180.00 -131.65 -48.35 0 5.00e+00 4.00e-02 9.35e+01 dihedral pdb=" CA GLU A 682 " pdb=" C GLU A 682 " pdb=" N GLU A 683 " pdb=" CA GLU A 683 " ideal model delta harmonic sigma weight residual -180.00 -131.67 -48.33 0 5.00e+00 4.00e-02 9.34e+01 dihedral pdb=" CB CYS C 457 " pdb=" SG CYS C 457 " pdb=" SG CYS C 476 " pdb=" CB CYS C 476 " ideal model delta sinusoidal sigma weight residual -86.00 -166.39 80.39 1 1.00e+01 1.00e-02 8.00e+01 ... (remaining 13781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 3514 0.083 - 0.167: 387 0.167 - 0.250: 13 0.250 - 0.334: 0 0.334 - 0.417: 2 Chirality restraints: 3916 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-02 2.50e+03 4.36e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-02 2.50e+03 4.31e+02 chirality pdb=" CB ILE A 688 " pdb=" CA ILE A 688 " pdb=" CG1 ILE A 688 " pdb=" CG2 ILE A 688 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 3913 not shown) Planarity restraints: 4082 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 680 " -0.046 5.00e-02 4.00e+02 7.02e-02 7.89e+00 pdb=" N PRO C 681 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO C 681 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 681 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 680 " 0.046 5.00e-02 4.00e+02 7.02e-02 7.89e+00 pdb=" N PRO A 681 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 681 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 681 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 105 " 0.044 5.00e-02 4.00e+02 6.66e-02 7.09e+00 pdb=" N PRO C 106 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 106 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 106 " 0.037 5.00e-02 4.00e+02 ... (remaining 4079 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 694 2.65 - 3.21: 25238 3.21 - 3.78: 33832 3.78 - 4.34: 42339 4.34 - 4.90: 67124 Nonbonded interactions: 169227 Sorted by model distance: nonbonded pdb=" O LEU D 567 " pdb=" OG SER D 570 " model vdw 2.088 3.040 nonbonded pdb=" O LEU B 567 " pdb=" OG SER B 570 " model vdw 2.088 3.040 nonbonded pdb=" O PHE A 102 " pdb=" OG1 THR A 105 " model vdw 2.116 3.040 nonbonded pdb=" O PHE C 102 " pdb=" OG1 THR C 105 " model vdw 2.117 3.040 nonbonded pdb=" OG1 THR B 410 " pdb=" N LEU B 411 " model vdw 2.131 3.120 ... (remaining 169222 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.350 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 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 : 0.010 0.079 23384 Z= 0.452 Angle : 0.972 22.881 32090 Z= 0.520 Chirality : 0.051 0.417 3916 Planarity : 0.006 0.070 4072 Dihedral : 14.542 119.249 7812 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.63 % Favored : 83.37 % Rotamer: Outliers : 0.82 % Allowed : 14.22 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.97 (0.12), residues: 3144 helix: -2.67 (0.11), residues: 1212 sheet: -3.46 (0.22), residues: 378 loop : -3.83 (0.13), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 742 TYR 0.034 0.002 TYR B 731 PHE 0.023 0.003 PHE C 550 TRP 0.012 0.002 TRP D 772 HIS 0.007 0.002 HIS B 703 Details of bonding type rmsd covalent geometry : bond 0.00976 (23356) covalent geometry : angle 0.93847 (32022) SS BOND : bond 0.01072 ( 16) SS BOND : angle 1.72128 ( 32) hydrogen bonds : bond 0.15611 ( 1038) hydrogen bonds : angle 7.87156 ( 2946) link_BETA1-4 : bond 0.06499 ( 2) link_BETA1-4 : angle 17.88684 ( 6) link_NAG-ASN : bond 0.00508 ( 10) link_NAG-ASN : angle 1.71680 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 230 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 683 GLU cc_start: 0.5063 (pp20) cc_final: 0.4220 (mp0) REVERT: A 688 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8089 (mm) REVERT: A 727 MET cc_start: 0.7051 (ttm) cc_final: 0.6834 (ttm) REVERT: B 410 THR cc_start: 0.9531 (OUTLIER) cc_final: 0.9291 (p) REVERT: C 727 MET cc_start: 0.7200 (ttm) cc_final: 0.6971 (ttm) REVERT: D 160 ILE cc_start: 0.8906 (tt) cc_final: 0.8683 (tt) outliers start: 18 outliers final: 8 residues processed: 246 average time/residue: 0.1312 time to fit residues: 55.2895 Evaluate side-chains 182 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 172 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 794 SER Chi-restraints excluded: chain D residue 410 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 40.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 0.5980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 134 HIS A 162 HIS A 171 HIS A 177 GLN A 217 GLN A 294 ASN A 414 GLN A 530 GLN A 731 ASN A 801 HIS ** A 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 GLN B 333 ASN B 368 ASN B 486 HIS B 656 GLN B 697 ASN C 47 ASN ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 HIS C 171 HIS C 177 GLN C 217 GLN C 294 ASN C 530 GLN C 731 ASN C 801 HIS ** C 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 GLN D 333 ASN D 368 ASN D 486 HIS D 649 ASN D 656 GLN D 697 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.090388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.067835 restraints weight = 80098.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.068218 restraints weight = 47549.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.068690 restraints weight = 35865.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.069241 restraints weight = 32500.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.069291 restraints weight = 28971.664| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 23384 Z= 0.179 Angle : 0.717 8.529 32090 Z= 0.377 Chirality : 0.046 0.271 3916 Planarity : 0.005 0.064 4072 Dihedral : 8.134 102.022 3577 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 2.69 % Allowed : 17.05 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.33 (0.14), residues: 3144 helix: -0.88 (0.14), residues: 1250 sheet: -2.64 (0.25), residues: 348 loop : -3.34 (0.14), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 693 TYR 0.018 0.001 TYR D 282 PHE 0.018 0.002 PHE B 642 TRP 0.012 0.001 TRP C 789 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00403 (23356) covalent geometry : angle 0.71390 (32022) SS BOND : bond 0.00506 ( 16) SS BOND : angle 1.81618 ( 32) hydrogen bonds : bond 0.04971 ( 1038) hydrogen bonds : angle 5.70889 ( 2946) link_BETA1-4 : bond 0.00443 ( 2) link_BETA1-4 : angle 1.34920 ( 6) link_NAG-ASN : bond 0.00239 ( 10) link_NAG-ASN : angle 1.53225 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 208 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.8758 (mmm) cc_final: 0.8167 (mmm) REVERT: A 683 GLU cc_start: 0.5879 (pp20) cc_final: 0.4607 (mp0) REVERT: A 688 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8577 (mm) REVERT: A 727 MET cc_start: 0.8751 (ttm) cc_final: 0.8518 (ttm) REVERT: B 228 ILE cc_start: 0.9537 (mt) cc_final: 0.9148 (tt) REVERT: B 561 MET cc_start: 0.8304 (mtp) cc_final: 0.8090 (mtp) REVERT: B 565 MET cc_start: 0.8547 (tmm) cc_final: 0.8140 (tmm) REVERT: B 653 PHE cc_start: 0.8580 (t80) cc_final: 0.8224 (t80) REVERT: C 230 MET cc_start: 0.8400 (mmm) cc_final: 0.8018 (mmm) REVERT: C 727 MET cc_start: 0.8789 (ttm) cc_final: 0.8552 (ttm) REVERT: C 820 ASP cc_start: 0.8478 (t70) cc_final: 0.8251 (t70) REVERT: D 132 MET cc_start: 0.8564 (mmp) cc_final: 0.8335 (mmt) REVERT: D 142 MET cc_start: 0.8647 (mmm) cc_final: 0.8432 (mmm) REVERT: D 562 MET cc_start: 0.9047 (tmm) cc_final: 0.8819 (tmm) REVERT: D 565 MET cc_start: 0.8258 (tmm) cc_final: 0.7797 (tmm) outliers start: 59 outliers final: 34 residues processed: 255 average time/residue: 0.1161 time to fit residues: 52.1835 Evaluate side-chains 220 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 822 ARG Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 700 PHE Chi-restraints excluded: chain C residue 794 SER Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 825 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 258 optimal weight: 0.0770 chunk 308 optimal weight: 8.9990 chunk 242 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 chunk 253 optimal weight: 30.0000 chunk 164 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 241 optimal weight: 8.9990 chunk 220 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 801 HIS ** A 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 HIS ** C 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.089495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.066941 restraints weight = 79931.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.067439 restraints weight = 46553.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.068046 restraints weight = 34963.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.068254 restraints weight = 31475.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.068413 restraints weight = 28207.925| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 23384 Z= 0.201 Angle : 0.686 9.823 32090 Z= 0.358 Chirality : 0.046 0.330 3916 Planarity : 0.005 0.061 4072 Dihedral : 7.742 98.606 3573 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.27 % Favored : 89.73 % Rotamer: Outliers : 3.56 % Allowed : 18.96 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.14), residues: 3144 helix: -0.19 (0.14), residues: 1240 sheet: -2.53 (0.25), residues: 372 loop : -3.06 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 544 TYR 0.018 0.001 TYR D 282 PHE 0.024 0.002 PHE D 653 TRP 0.010 0.001 TRP D 772 HIS 0.016 0.001 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00458 (23356) covalent geometry : angle 0.68298 (32022) SS BOND : bond 0.00465 ( 16) SS BOND : angle 1.68613 ( 32) hydrogen bonds : bond 0.04708 ( 1038) hydrogen bonds : angle 5.36295 ( 2946) link_BETA1-4 : bond 0.00195 ( 2) link_BETA1-4 : angle 1.47482 ( 6) link_NAG-ASN : bond 0.00246 ( 10) link_NAG-ASN : angle 1.36085 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 195 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 628 MET cc_start: 0.8085 (tmm) cc_final: 0.7672 (tmm) REVERT: A 683 GLU cc_start: 0.5825 (pp20) cc_final: 0.4997 (mp0) REVERT: A 688 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8624 (mm) REVERT: A 727 MET cc_start: 0.8764 (ttm) cc_final: 0.8555 (ttm) REVERT: B 228 ILE cc_start: 0.9487 (mt) cc_final: 0.9074 (tt) REVERT: B 478 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9102 (tt) REVERT: B 493 THR cc_start: 0.9068 (OUTLIER) cc_final: 0.8733 (p) REVERT: B 561 MET cc_start: 0.8478 (mtp) cc_final: 0.8189 (mtp) REVERT: B 565 MET cc_start: 0.8673 (tmm) cc_final: 0.8231 (tmm) REVERT: C 230 MET cc_start: 0.8443 (mmm) cc_final: 0.8066 (mmm) REVERT: C 628 MET cc_start: 0.8112 (tmm) cc_final: 0.7820 (tmm) REVERT: D 132 MET cc_start: 0.8606 (mmp) cc_final: 0.8375 (mmt) REVERT: D 142 MET cc_start: 0.8674 (mmm) cc_final: 0.8460 (mmm) REVERT: D 478 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9034 (tt) REVERT: D 493 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8777 (p) REVERT: D 561 MET cc_start: 0.8366 (mtp) cc_final: 0.7964 (mtp) REVERT: D 562 MET cc_start: 0.9012 (tmm) cc_final: 0.8771 (tmm) REVERT: D 565 MET cc_start: 0.8357 (tmm) cc_final: 0.7542 (tmm) REVERT: D 706 MET cc_start: 0.8323 (tpp) cc_final: 0.7732 (tpp) outliers start: 78 outliers final: 47 residues processed: 255 average time/residue: 0.1161 time to fit residues: 52.9039 Evaluate side-chains 241 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 189 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 667 SER Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 700 PHE Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 794 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 825 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 165 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 204 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 24 optimal weight: 0.0030 chunk 310 optimal weight: 0.0270 chunk 4 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 213 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 overall best weight: 0.7050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 HIS A 824 ASN C 134 HIS C 498 HIS ** C 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.092763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.070517 restraints weight = 78671.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.071093 restraints weight = 44442.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.071720 restraints weight = 32803.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.072042 restraints weight = 29980.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.072120 restraints weight = 26492.879| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 23384 Z= 0.116 Angle : 0.617 12.102 32090 Z= 0.320 Chirality : 0.045 0.368 3916 Planarity : 0.004 0.058 4072 Dihedral : 7.137 95.236 3573 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 3.56 % Allowed : 20.56 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.15), residues: 3144 helix: 0.31 (0.15), residues: 1250 sheet: -2.43 (0.24), residues: 406 loop : -2.64 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 544 TYR 0.019 0.001 TYR D 282 PHE 0.022 0.001 PHE D 653 TRP 0.016 0.001 TRP B 635 HIS 0.004 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00242 (23356) covalent geometry : angle 0.61463 (32022) SS BOND : bond 0.00376 ( 16) SS BOND : angle 1.41718 ( 32) hydrogen bonds : bond 0.03719 ( 1038) hydrogen bonds : angle 4.80737 ( 2946) link_BETA1-4 : bond 0.00359 ( 2) link_BETA1-4 : angle 1.05435 ( 6) link_NAG-ASN : bond 0.00112 ( 10) link_NAG-ASN : angle 1.30494 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 215 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 292 LEU cc_start: 0.8713 (tp) cc_final: 0.8434 (tt) REVERT: A 628 MET cc_start: 0.8115 (tmm) cc_final: 0.7674 (tmm) REVERT: A 683 GLU cc_start: 0.6313 (pp20) cc_final: 0.5592 (mp0) REVERT: A 688 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8580 (mm) REVERT: B 551 LEU cc_start: 0.9301 (mt) cc_final: 0.9068 (mt) REVERT: B 561 MET cc_start: 0.8506 (mtp) cc_final: 0.8201 (mtp) REVERT: B 565 MET cc_start: 0.8611 (tmm) cc_final: 0.8112 (tmm) REVERT: B 630 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.9037 (mm) REVERT: B 706 MET cc_start: 0.8285 (tpp) cc_final: 0.7962 (mmm) REVERT: C 292 LEU cc_start: 0.8633 (tp) cc_final: 0.8322 (tt) REVERT: C 628 MET cc_start: 0.8022 (tmm) cc_final: 0.7683 (tmm) REVERT: D 562 MET cc_start: 0.9044 (tmm) cc_final: 0.8791 (tmm) REVERT: D 565 MET cc_start: 0.8309 (tmm) cc_final: 0.7535 (tmm) REVERT: D 630 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8864 (mm) REVERT: D 654 MET cc_start: 0.8608 (tpp) cc_final: 0.8292 (mtp) outliers start: 78 outliers final: 46 residues processed: 273 average time/residue: 0.1235 time to fit residues: 59.1218 Evaluate side-chains 251 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 202 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 700 PHE Chi-restraints excluded: chain C residue 709 SER Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 777 SER Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 825 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 82 optimal weight: 9.9990 chunk 178 optimal weight: 20.0000 chunk 304 optimal weight: 5.9990 chunk 262 optimal weight: 7.9990 chunk 174 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 158 optimal weight: 6.9990 chunk 252 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 HIS ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN B 697 ASN C 425 HIS ** C 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 697 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.089320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.066906 restraints weight = 80074.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.067005 restraints weight = 49207.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.067742 restraints weight = 38195.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.068157 restraints weight = 33191.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.068284 restraints weight = 29770.064| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 23384 Z= 0.254 Angle : 0.697 12.948 32090 Z= 0.363 Chirality : 0.046 0.409 3916 Planarity : 0.005 0.057 4072 Dihedral : 7.154 90.424 3572 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 4.92 % Allowed : 21.15 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.15), residues: 3144 helix: 0.40 (0.14), residues: 1228 sheet: -2.50 (0.24), residues: 396 loop : -2.63 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 233 TYR 0.018 0.002 TYR D 731 PHE 0.025 0.002 PHE B 653 TRP 0.012 0.001 TRP B 772 HIS 0.004 0.001 HIS C 801 Details of bonding type rmsd covalent geometry : bond 0.00581 (23356) covalent geometry : angle 0.69329 (32022) SS BOND : bond 0.00461 ( 16) SS BOND : angle 1.70214 ( 32) hydrogen bonds : bond 0.04568 ( 1038) hydrogen bonds : angle 5.06823 ( 2946) link_BETA1-4 : bond 0.00080 ( 2) link_BETA1-4 : angle 1.31501 ( 6) link_NAG-ASN : bond 0.00346 ( 10) link_NAG-ASN : angle 1.58075 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 201 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 628 MET cc_start: 0.8281 (tmm) cc_final: 0.7913 (tmm) REVERT: A 688 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8400 (mt) REVERT: A 820 ASP cc_start: 0.8562 (t0) cc_final: 0.8134 (t70) REVERT: B 386 MET cc_start: 0.7523 (ptp) cc_final: 0.7254 (ptm) REVERT: B 478 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9037 (tt) REVERT: B 493 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8670 (p) REVERT: B 561 MET cc_start: 0.8511 (mtp) cc_final: 0.8172 (mtp) REVERT: B 565 MET cc_start: 0.8656 (tmm) cc_final: 0.8149 (tmm) REVERT: B 653 PHE cc_start: 0.8606 (t80) cc_final: 0.8293 (t80) REVERT: C 628 MET cc_start: 0.8260 (tmm) cc_final: 0.7879 (tmm) REVERT: D 386 MET cc_start: 0.7346 (ptm) cc_final: 0.6947 (ptt) REVERT: D 478 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9031 (tt) REVERT: D 493 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8691 (p) REVERT: D 562 MET cc_start: 0.9028 (tmm) cc_final: 0.8724 (tmm) REVERT: D 565 MET cc_start: 0.8446 (tmm) cc_final: 0.7700 (tmm) outliers start: 108 outliers final: 74 residues processed: 288 average time/residue: 0.1117 time to fit residues: 57.1237 Evaluate side-chains 273 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 194 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 822 ARG Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 700 PHE Chi-restraints excluded: chain C residue 709 SER Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 727 MET Chi-restraints excluded: chain C residue 777 SER Chi-restraints excluded: chain C residue 794 SER Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 849 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 617 SER Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 825 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 102 optimal weight: 2.9990 chunk 153 optimal weight: 20.0000 chunk 217 optimal weight: 0.7980 chunk 254 optimal weight: 10.0000 chunk 216 optimal weight: 0.9980 chunk 241 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 283 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 234 optimal weight: 5.9990 chunk 258 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.091814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.069328 restraints weight = 79162.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.069924 restraints weight = 46577.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.070479 restraints weight = 34448.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.070832 restraints weight = 31556.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.070930 restraints weight = 28000.783| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 23384 Z= 0.132 Angle : 0.622 13.996 32090 Z= 0.320 Chirality : 0.045 0.380 3916 Planarity : 0.004 0.057 4072 Dihedral : 6.887 87.911 3572 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 4.24 % Allowed : 21.51 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.15), residues: 3144 helix: 0.54 (0.15), residues: 1262 sheet: -2.38 (0.24), residues: 404 loop : -2.42 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 233 TYR 0.018 0.001 TYR B 282 PHE 0.030 0.001 PHE D 653 TRP 0.010 0.001 TRP D 772 HIS 0.003 0.001 HIS C 425 Details of bonding type rmsd covalent geometry : bond 0.00293 (23356) covalent geometry : angle 0.61727 (32022) SS BOND : bond 0.00413 ( 16) SS BOND : angle 1.99229 ( 32) hydrogen bonds : bond 0.03808 ( 1038) hydrogen bonds : angle 4.71552 ( 2946) link_BETA1-4 : bond 0.00185 ( 2) link_BETA1-4 : angle 1.05258 ( 6) link_NAG-ASN : bond 0.00137 ( 10) link_NAG-ASN : angle 1.51267 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 203 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: A 292 LEU cc_start: 0.8753 (tp) cc_final: 0.8468 (tt) REVERT: A 549 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: A 628 MET cc_start: 0.8127 (tmm) cc_final: 0.7672 (tmm) REVERT: A 820 ASP cc_start: 0.8442 (t0) cc_final: 0.8055 (t70) REVERT: B 157 MET cc_start: 0.8120 (ttt) cc_final: 0.7889 (tmm) REVERT: B 386 MET cc_start: 0.7581 (ptp) cc_final: 0.7263 (ptm) REVERT: B 478 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9018 (tt) REVERT: B 493 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8611 (p) REVERT: B 561 MET cc_start: 0.8506 (mtp) cc_final: 0.8127 (mtp) REVERT: B 565 MET cc_start: 0.8614 (tmm) cc_final: 0.8158 (tmm) REVERT: B 630 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8856 (mm) REVERT: B 653 PHE cc_start: 0.8572 (t80) cc_final: 0.8282 (t80) REVERT: C 292 LEU cc_start: 0.8674 (tp) cc_final: 0.8358 (tt) REVERT: C 549 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7600 (mp0) REVERT: C 628 MET cc_start: 0.8098 (tmm) cc_final: 0.7716 (tmm) REVERT: D 386 MET cc_start: 0.7554 (ptm) cc_final: 0.7125 (ptt) REVERT: D 478 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9040 (tt) REVERT: D 493 THR cc_start: 0.9004 (OUTLIER) cc_final: 0.8647 (p) REVERT: D 562 MET cc_start: 0.9042 (tmm) cc_final: 0.8735 (tmm) REVERT: D 565 MET cc_start: 0.8368 (tmm) cc_final: 0.7658 (tmm) outliers start: 93 outliers final: 66 residues processed: 277 average time/residue: 0.1087 time to fit residues: 53.9133 Evaluate side-chains 268 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 195 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 218 PHE Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 461 CYS Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 218 PHE Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 549 GLU Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 700 PHE Chi-restraints excluded: chain C residue 709 SER Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 727 MET Chi-restraints excluded: chain C residue 777 SER Chi-restraints excluded: chain C residue 794 SER Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 461 CYS Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 617 SER Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 825 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 198 optimal weight: 0.9990 chunk 129 optimal weight: 10.0000 chunk 312 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 263 optimal weight: 40.0000 chunk 274 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 31 optimal weight: 30.0000 chunk 152 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 671 ASN C 824 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.092374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.069829 restraints weight = 79391.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.070431 restraints weight = 46638.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.071041 restraints weight = 34306.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.071329 restraints weight = 31647.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.071461 restraints weight = 27961.206| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 23384 Z= 0.123 Angle : 0.610 14.231 32090 Z= 0.311 Chirality : 0.044 0.383 3916 Planarity : 0.004 0.054 4072 Dihedral : 6.527 80.742 3570 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 4.38 % Allowed : 22.01 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.15), residues: 3144 helix: 0.70 (0.15), residues: 1262 sheet: -2.19 (0.25), residues: 416 loop : -2.29 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 233 TYR 0.018 0.001 TYR D 282 PHE 0.026 0.001 PHE D 653 TRP 0.008 0.001 TRP B 772 HIS 0.003 0.001 HIS C 425 Details of bonding type rmsd covalent geometry : bond 0.00280 (23356) covalent geometry : angle 0.60538 (32022) SS BOND : bond 0.00391 ( 16) SS BOND : angle 1.82782 ( 32) hydrogen bonds : bond 0.03645 ( 1038) hydrogen bonds : angle 4.59065 ( 2946) link_BETA1-4 : bond 0.00177 ( 2) link_BETA1-4 : angle 1.05826 ( 6) link_NAG-ASN : bond 0.00130 ( 10) link_NAG-ASN : angle 1.69792 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 208 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 628 MET cc_start: 0.8107 (tmm) cc_final: 0.7700 (tmm) REVERT: A 682 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7638 (mp0) REVERT: A 820 ASP cc_start: 0.8400 (t0) cc_final: 0.8035 (t70) REVERT: B 386 MET cc_start: 0.7522 (ptp) cc_final: 0.7169 (ptm) REVERT: B 478 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9014 (tt) REVERT: B 493 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8608 (p) REVERT: B 561 MET cc_start: 0.8515 (mtp) cc_final: 0.8140 (mtp) REVERT: B 565 MET cc_start: 0.8608 (tmm) cc_final: 0.8189 (tmm) REVERT: B 653 PHE cc_start: 0.8496 (t80) cc_final: 0.8057 (t80) REVERT: B 706 MET cc_start: 0.7909 (mmm) cc_final: 0.7489 (tpt) REVERT: C 628 MET cc_start: 0.8101 (tmm) cc_final: 0.7714 (tmm) REVERT: D 132 MET cc_start: 0.8445 (mmp) cc_final: 0.8147 (mmp) REVERT: D 386 MET cc_start: 0.7695 (ptm) cc_final: 0.7379 (ptt) REVERT: D 478 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9103 (tt) REVERT: D 493 THR cc_start: 0.8966 (OUTLIER) cc_final: 0.8618 (p) REVERT: D 562 MET cc_start: 0.9070 (tmm) cc_final: 0.8722 (tmm) REVERT: D 565 MET cc_start: 0.8421 (tmm) cc_final: 0.7722 (tmm) REVERT: D 630 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8969 (mm) REVERT: D 831 LEU cc_start: 0.8456 (pp) cc_final: 0.8209 (tt) outliers start: 96 outliers final: 70 residues processed: 288 average time/residue: 0.1069 time to fit residues: 54.9978 Evaluate side-chains 277 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 202 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain B residue 461 CYS Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 700 PHE Chi-restraints excluded: chain C residue 709 SER Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 727 MET Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 777 SER Chi-restraints excluded: chain C residue 794 SER Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 849 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 461 CYS Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 695 ILE Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 825 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 54 optimal weight: 0.9980 chunk 287 optimal weight: 7.9990 chunk 64 optimal weight: 0.3980 chunk 94 optimal weight: 9.9990 chunk 113 optimal weight: 0.0870 chunk 150 optimal weight: 6.9990 chunk 17 optimal weight: 0.0570 chunk 217 optimal weight: 1.9990 chunk 240 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 6 optimal weight: 0.0670 overall best weight: 0.3214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.094382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.072052 restraints weight = 78402.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.072725 restraints weight = 44992.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.073346 restraints weight = 33139.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.073713 restraints weight = 28730.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.073799 restraints weight = 26332.166| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 23384 Z= 0.107 Angle : 0.611 14.930 32090 Z= 0.306 Chirality : 0.044 0.393 3916 Planarity : 0.004 0.057 4072 Dihedral : 6.086 71.638 3570 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.24 % Allowed : 23.56 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.15), residues: 3144 helix: 0.82 (0.15), residues: 1274 sheet: -1.98 (0.25), residues: 412 loop : -2.17 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 233 TYR 0.019 0.001 TYR B 282 PHE 0.027 0.001 PHE D 653 TRP 0.016 0.001 TRP C 629 HIS 0.003 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00228 (23356) covalent geometry : angle 0.60663 (32022) SS BOND : bond 0.00329 ( 16) SS BOND : angle 1.55985 ( 32) hydrogen bonds : bond 0.03304 ( 1038) hydrogen bonds : angle 4.44863 ( 2946) link_BETA1-4 : bond 0.00312 ( 2) link_BETA1-4 : angle 0.94326 ( 6) link_NAG-ASN : bond 0.00089 ( 10) link_NAG-ASN : angle 1.90561 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 225 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 628 MET cc_start: 0.8071 (tmm) cc_final: 0.7667 (tmm) REVERT: A 698 ASP cc_start: 0.8240 (m-30) cc_final: 0.7851 (t0) REVERT: B 162 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8291 (mm-30) REVERT: B 386 MET cc_start: 0.7401 (ptp) cc_final: 0.7045 (ptm) REVERT: B 478 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9039 (tt) REVERT: B 493 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8566 (p) REVERT: B 561 MET cc_start: 0.8607 (mtp) cc_final: 0.8238 (mtp) REVERT: B 565 MET cc_start: 0.8661 (tmm) cc_final: 0.8306 (tmm) REVERT: B 653 PHE cc_start: 0.8509 (t80) cc_final: 0.8168 (t80) REVERT: B 706 MET cc_start: 0.8045 (mmm) cc_final: 0.7641 (tpt) REVERT: B 831 LEU cc_start: 0.8221 (pp) cc_final: 0.8011 (tt) REVERT: C 628 MET cc_start: 0.8093 (tmm) cc_final: 0.7710 (tmm) REVERT: C 698 ASP cc_start: 0.8214 (m-30) cc_final: 0.8010 (t0) REVERT: D 157 MET cc_start: 0.8187 (ttp) cc_final: 0.7949 (tmm) REVERT: D 386 MET cc_start: 0.7531 (ptm) cc_final: 0.7174 (ptt) REVERT: D 478 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.8982 (tt) REVERT: D 493 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8568 (p) REVERT: D 562 MET cc_start: 0.9107 (tmm) cc_final: 0.8759 (tmm) REVERT: D 565 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.7774 (tmm) REVERT: D 630 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.9061 (mm) REVERT: D 831 LEU cc_start: 0.8414 (pp) cc_final: 0.8182 (tt) outliers start: 71 outliers final: 55 residues processed: 282 average time/residue: 0.1174 time to fit residues: 58.6769 Evaluate side-chains 268 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 207 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain B residue 461 CYS Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 700 PHE Chi-restraints excluded: chain C residue 709 SER Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 727 MET Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 461 CYS Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 825 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 51 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 270 optimal weight: 5.9990 chunk 234 optimal weight: 0.9990 chunk 259 optimal weight: 0.0970 chunk 298 optimal weight: 2.9990 chunk 265 optimal weight: 0.2980 chunk 201 optimal weight: 4.9990 chunk 1 optimal weight: 20.0000 chunk 278 optimal weight: 1.9990 chunk 100 optimal weight: 20.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN B 95 GLN C 217 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.094152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.071882 restraints weight = 79006.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.072450 restraints weight = 46883.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.073300 restraints weight = 33787.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.073486 restraints weight = 29888.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.073581 restraints weight = 26516.029| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 23384 Z= 0.109 Angle : 0.613 14.776 32090 Z= 0.308 Chirality : 0.044 0.397 3916 Planarity : 0.004 0.058 4072 Dihedral : 5.729 59.999 3570 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.60 % Allowed : 23.75 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.15), residues: 3144 helix: 0.88 (0.15), residues: 1278 sheet: -1.84 (0.26), residues: 412 loop : -2.09 (0.16), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 233 TYR 0.018 0.001 TYR B 282 PHE 0.028 0.001 PHE D 653 TRP 0.011 0.001 TRP D 197 HIS 0.003 0.000 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00245 (23356) covalent geometry : angle 0.60762 (32022) SS BOND : bond 0.00324 ( 16) SS BOND : angle 1.59819 ( 32) hydrogen bonds : bond 0.03387 ( 1038) hydrogen bonds : angle 4.44417 ( 2946) link_BETA1-4 : bond 0.00231 ( 2) link_BETA1-4 : angle 1.07117 ( 6) link_NAG-ASN : bond 0.00126 ( 10) link_NAG-ASN : angle 2.22392 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 209 time to evaluate : 0.943 Fit side-chains REVERT: A 480 CYS cc_start: 0.8289 (p) cc_final: 0.7884 (p) REVERT: A 628 MET cc_start: 0.8130 (tmm) cc_final: 0.7739 (tmm) REVERT: A 698 ASP cc_start: 0.8159 (m-30) cc_final: 0.7839 (t0) REVERT: A 820 ASP cc_start: 0.8413 (t0) cc_final: 0.8030 (t0) REVERT: B 386 MET cc_start: 0.7391 (ptp) cc_final: 0.6979 (ptm) REVERT: B 478 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9008 (tt) REVERT: B 493 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8598 (p) REVERT: B 561 MET cc_start: 0.8648 (mtp) cc_final: 0.8269 (mtp) REVERT: B 565 MET cc_start: 0.8670 (tmm) cc_final: 0.8344 (tmm) REVERT: B 653 PHE cc_start: 0.8508 (t80) cc_final: 0.8074 (t80) REVERT: B 706 MET cc_start: 0.8006 (mmm) cc_final: 0.7611 (tpt) REVERT: C 480 CYS cc_start: 0.8279 (p) cc_final: 0.7853 (p) REVERT: C 628 MET cc_start: 0.8117 (tmm) cc_final: 0.7726 (tmm) REVERT: D 229 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7916 (mm) REVERT: D 386 MET cc_start: 0.7529 (ptm) cc_final: 0.7142 (ptt) REVERT: D 478 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9039 (tt) REVERT: D 493 THR cc_start: 0.8907 (OUTLIER) cc_final: 0.8582 (p) REVERT: D 561 MET cc_start: 0.8643 (mtp) cc_final: 0.8288 (mtp) REVERT: D 562 MET cc_start: 0.9137 (tmm) cc_final: 0.8766 (tmm) REVERT: D 565 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.7778 (tmm) REVERT: D 630 ILE cc_start: 0.9385 (OUTLIER) cc_final: 0.9183 (mm) REVERT: D 831 LEU cc_start: 0.8378 (pp) cc_final: 0.8141 (tt) outliers start: 79 outliers final: 61 residues processed: 272 average time/residue: 0.1205 time to fit residues: 58.3171 Evaluate side-chains 271 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 203 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain B residue 461 CYS Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 700 PHE Chi-restraints excluded: chain C residue 709 SER Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 727 MET Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 849 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 461 CYS Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 617 SER Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 825 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 40 optimal weight: 0.8980 chunk 254 optimal weight: 0.0870 chunk 128 optimal weight: 6.9990 chunk 265 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 141 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 211 optimal weight: 0.9980 chunk 138 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.095077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.072792 restraints weight = 78887.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.073569 restraints weight = 44439.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.074107 restraints weight = 32903.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.074447 restraints weight = 28548.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.074553 restraints weight = 26430.285| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 23384 Z= 0.107 Angle : 0.616 15.301 32090 Z= 0.309 Chirality : 0.044 0.404 3916 Planarity : 0.004 0.058 4072 Dihedral : 5.364 46.416 3570 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.14 % Allowed : 24.34 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.15), residues: 3144 helix: 0.95 (0.15), residues: 1266 sheet: -1.70 (0.26), residues: 420 loop : -2.01 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 233 TYR 0.019 0.001 TYR B 282 PHE 0.029 0.001 PHE D 653 TRP 0.011 0.001 TRP D 166 HIS 0.003 0.000 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00238 (23356) covalent geometry : angle 0.61055 (32022) SS BOND : bond 0.00289 ( 16) SS BOND : angle 1.45048 ( 32) hydrogen bonds : bond 0.03250 ( 1038) hydrogen bonds : angle 4.39815 ( 2946) link_BETA1-4 : bond 0.00301 ( 2) link_BETA1-4 : angle 1.04125 ( 6) link_NAG-ASN : bond 0.00165 ( 10) link_NAG-ASN : angle 2.44468 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 214 time to evaluate : 0.938 Fit side-chains REVERT: A 480 CYS cc_start: 0.8313 (p) cc_final: 0.7815 (p) REVERT: A 572 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7276 (mt) REVERT: A 628 MET cc_start: 0.8109 (tmm) cc_final: 0.7722 (tmm) REVERT: A 698 ASP cc_start: 0.8127 (m-30) cc_final: 0.7814 (t0) REVERT: B 386 MET cc_start: 0.7289 (ptp) cc_final: 0.6875 (ptm) REVERT: B 478 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8999 (tt) REVERT: B 493 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8524 (p) REVERT: B 561 MET cc_start: 0.8623 (mtp) cc_final: 0.8258 (mtp) REVERT: B 565 MET cc_start: 0.8654 (tmm) cc_final: 0.8343 (tmm) REVERT: B 653 PHE cc_start: 0.8598 (t80) cc_final: 0.8151 (t80) REVERT: B 706 MET cc_start: 0.7996 (mmm) cc_final: 0.7614 (tpt) REVERT: B 814 ASP cc_start: 0.8594 (t0) cc_final: 0.8104 (m-30) REVERT: C 480 CYS cc_start: 0.8345 (p) cc_final: 0.7836 (p) REVERT: C 597 MET cc_start: 0.9186 (tpp) cc_final: 0.8806 (ttt) REVERT: C 628 MET cc_start: 0.8103 (tmm) cc_final: 0.7703 (tmm) REVERT: D 386 MET cc_start: 0.7369 (ptm) cc_final: 0.6866 (ptt) REVERT: D 478 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9013 (tt) REVERT: D 493 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8553 (p) REVERT: D 561 MET cc_start: 0.8582 (mtp) cc_final: 0.8243 (mtp) REVERT: D 562 MET cc_start: 0.9144 (tmm) cc_final: 0.8890 (tmm) REVERT: D 565 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.7789 (tmm) REVERT: D 831 LEU cc_start: 0.8397 (pp) cc_final: 0.8163 (tt) outliers start: 69 outliers final: 59 residues processed: 268 average time/residue: 0.1204 time to fit residues: 57.5109 Evaluate side-chains 271 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 206 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 700 PHE Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 801 HIS Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 461 CYS Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 700 PHE Chi-restraints excluded: chain C residue 709 SER Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 727 MET Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 794 SER Chi-restraints excluded: chain C residue 801 HIS Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 849 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 282 TYR Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 461 CYS Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 565 MET Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 825 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 93 optimal weight: 0.9990 chunk 131 optimal weight: 10.0000 chunk 288 optimal weight: 7.9990 chunk 168 optimal weight: 9.9990 chunk 193 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 156 optimal weight: 0.6980 chunk 180 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.095016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.072700 restraints weight = 79254.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.073164 restraints weight = 46626.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.074004 restraints weight = 34115.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.074422 restraints weight = 29015.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.074431 restraints weight = 26214.225| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 23384 Z= 0.108 Angle : 0.610 14.570 32090 Z= 0.306 Chirality : 0.044 0.383 3916 Planarity : 0.004 0.058 4072 Dihedral : 5.119 38.317 3570 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.37 % Allowed : 24.11 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.15), residues: 3144 helix: 0.98 (0.15), residues: 1272 sheet: -1.60 (0.26), residues: 424 loop : -1.99 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 233 TYR 0.018 0.001 TYR B 282 PHE 0.030 0.001 PHE D 653 TRP 0.017 0.001 TRP A 629 HIS 0.003 0.000 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00243 (23356) covalent geometry : angle 0.60441 (32022) SS BOND : bond 0.00275 ( 16) SS BOND : angle 1.46383 ( 32) hydrogen bonds : bond 0.03234 ( 1038) hydrogen bonds : angle 4.36559 ( 2946) link_BETA1-4 : bond 0.00237 ( 2) link_BETA1-4 : angle 1.04600 ( 6) link_NAG-ASN : bond 0.00177 ( 10) link_NAG-ASN : angle 2.45859 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3272.89 seconds wall clock time: 57 minutes 25.06 seconds (3445.06 seconds total)