Starting phenix.real_space_refine on Sun Sep 13 10:58:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6whs_21674/09_2026/6whs_21674.cif Found real_map, /net/cci-nas-00/data/ceres_data/6whs_21674/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6whs_21674/09_2026/6whs_21674.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6whs_21674/09_2026/6whs_21674.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6whs_21674/09_2026/6whs_21674.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6whs_21674/09_2026/6whs_21674.map" model { file = "/net/cci-nas-00/data/ceres_data/6whs_21674/09_2026/6whs_21674.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6whs_21674/09_2026/6whs_21674.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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 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 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 chiralities: 2 Restraints were copied for chains: C, D, F Time building chain proxies: 9.19, per 1000 atoms: 0.40 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: 2.13 Conformation dependent library (CDL) restraints added in 990.1 milliseconds 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: 0.75 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: 5.05 Time building geometry restraints manager: 2.74 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 - 17.02: 12145 17.02 - 34.04: 1127 34.04 - 51.06: 200 51.06 - 68.08: 38 68.08 - 85.10: 22 Dihedral angle restraints: 13532 sinusoidal: 4354 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 13529 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: 0.05 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 26.130 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 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 : 14.127 85.096 7560 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/Z covalent geometry : bond 0.00976 / 0.45 (23356) covalent geometry : angle 0.93847 / 0.51 (32022) SS BOND : bond 0.01072 / 0.77 ( 16) SS BOND : angle 1.72128 / 1.18 ( 32) hydrogen bonds : bond 0.15611 / 10.46 ( 1038) hydrogen bonds : angle 7.87156 / 5.66 ( 2946) link_BETA1-4 : bond 0.06499 / 3.26 ( 2) link_BETA1-4 : angle 17.88684 / 9.28 ( 6) link_NAG-ASN : bond 0.00508 / 0.37 ( 10) link_NAG-ASN : angle 1.71680 / 1.07 ( 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 : 0.846 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: 0.1215 time to fit residues: 51.6185 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 : 0.883 ------------------------------------------------------------------------------- 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... 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 414 GLN 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: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.090466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.067915 restraints weight = 80097.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.068333 restraints weight = 47345.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.068791 restraints weight = 35615.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.069223 restraints weight = 32388.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.069289 restraints weight = 28939.078| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 23384 Z= 0.178 Angle : 0.713 8.513 32090 Z= 0.376 Chirality : 0.047 0.280 3916 Planarity : 0.005 0.064 4072 Dihedral : 6.655 55.701 3325 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 2.83 % Allowed : 17.05 % Favored : 80.13 % 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: -3.30 (0.14), residues: 3144 helix: -0.84 (0.14), residues: 1250 sheet: -2.63 (0.25), residues: 348 loop : -3.33 (0.14), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 693 TYR 0.019 0.001 TYR D 282 PHE 0.018 0.002 PHE B 642 TRP 0.013 0.001 TRP C 789 HIS 0.004 0.001 HIS A 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (23356) covalent geometry : angle 0.70964 / 0.38 (32022) SS BOND : bond 0.00781 / 0.40 ( 16) SS BOND : angle 1.91515 / 1.35 ( 32) hydrogen bonds : bond 0.04908 / 3.44 ( 1038) hydrogen bonds : angle 5.68068 / 4.07 ( 2946) link_BETA1-4 : bond 0.00585 / 0.29 ( 2) link_BETA1-4 : angle 1.32149 / 0.70 ( 6) link_NAG-ASN : bond 0.00315 / 0.22 ( 10) link_NAG-ASN : angle 1.33825 / 0.79 ( 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 272 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 210 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.8761 (mmm) cc_final: 0.8166 (mmm) REVERT: A 683 GLU cc_start: 0.5782 (pp20) cc_final: 0.4486 (mp0) REVERT: A 688 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8576 (mm) REVERT: A 727 MET cc_start: 0.8746 (ttm) cc_final: 0.8508 (ttm) REVERT: A 820 ASP cc_start: 0.8488 (t70) cc_final: 0.8246 (t70) REVERT: B 228 ILE cc_start: 0.9536 (mt) cc_final: 0.9147 (tt) REVERT: B 561 MET cc_start: 0.8319 (mtp) cc_final: 0.8091 (mtp) REVERT: B 565 MET cc_start: 0.8645 (tmm) cc_final: 0.8215 (tmm) REVERT: B 653 PHE cc_start: 0.8572 (t80) cc_final: 0.8258 (t80) REVERT: C 230 MET cc_start: 0.8412 (mmm) cc_final: 0.8020 (mmm) REVERT: C 414 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.8910 (pm20) REVERT: C 727 MET cc_start: 0.8788 (ttm) cc_final: 0.8549 (ttm) REVERT: C 820 ASP cc_start: 0.8501 (t70) cc_final: 0.8268 (t70) REVERT: D 132 MET cc_start: 0.8563 (mmp) cc_final: 0.8333 (mmt) REVERT: D 142 MET cc_start: 0.8650 (mmm) cc_final: 0.8441 (mmm) REVERT: D 562 MET cc_start: 0.9046 (tmm) cc_final: 0.8816 (tmm) REVERT: D 565 MET cc_start: 0.8276 (tmm) cc_final: 0.7802 (tmm) outliers start: 62 outliers final: 34 residues processed: 259 average time/residue: 0.1160 time to fit residues: 53.0642 Evaluate side-chains 223 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 414 GLN 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: 0.1980 chunk 308 optimal weight: 1.9990 chunk 242 optimal weight: 7.9990 chunk 175 optimal weight: 8.9990 chunk 253 optimal weight: 30.0000 chunk 164 optimal weight: 0.1980 chunk 64 optimal weight: 6.9990 chunk 241 optimal weight: 5.9990 chunk 220 optimal weight: 0.1980 chunk 7 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 801 HIS ** A 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS C 801 HIS ** C 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.090987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.068593 restraints weight = 79098.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.069130 restraints weight = 45419.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.069767 restraints weight = 33864.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.070071 restraints weight = 30773.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.070130 restraints weight = 27326.771| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 23384 Z= 0.138 Angle : 0.642 9.964 32090 Z= 0.337 Chirality : 0.045 0.313 3916 Planarity : 0.004 0.060 4072 Dihedral : 6.209 50.451 3321 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 3.14 % Allowed : 18.73 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.13 % 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: -2.54 (0.14), residues: 3144 helix: -0.09 (0.14), residues: 1252 sheet: -2.40 (0.25), residues: 372 loop : -2.96 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 822 TYR 0.018 0.001 TYR D 282 PHE 0.023 0.001 PHE D 653 TRP 0.008 0.001 TRP D 772 HIS 0.010 0.001 HIS C 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (23356) covalent geometry : angle 0.63978 / 0.34 (32022) SS BOND : bond 0.00401 / 0.26 ( 16) SS BOND : angle 1.59151 / 1.18 ( 32) hydrogen bonds : bond 0.04341 / 3.04 ( 1038) hydrogen bonds : angle 5.15109 / 3.69 ( 2946) link_BETA1-4 : bond 0.00222 / 0.12 ( 2) link_BETA1-4 : angle 1.37462 / 0.67 ( 6) link_NAG-ASN : bond 0.00205 / 0.15 ( 10) link_NAG-ASN : angle 1.01347 / 0.62 ( 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 269 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 200 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.8617 (mmm) cc_final: 0.8087 (mmm) REVERT: A 628 MET cc_start: 0.7951 (tmm) cc_final: 0.7548 (tmm) REVERT: A 683 GLU cc_start: 0.5829 (pp20) cc_final: 0.5150 (mp0) REVERT: A 688 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8531 (mm) REVERT: A 820 ASP cc_start: 0.8416 (t70) cc_final: 0.8088 (t70) REVERT: B 478 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8996 (tt) REVERT: B 493 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8703 (p) REVERT: B 561 MET cc_start: 0.8483 (mtp) cc_final: 0.8216 (mtp) REVERT: B 565 MET cc_start: 0.8633 (tmm) cc_final: 0.8102 (tmm) REVERT: C 480 CYS cc_start: 0.8258 (p) cc_final: 0.7927 (p) REVERT: C 628 MET cc_start: 0.7938 (tmm) cc_final: 0.7667 (tmm) REVERT: C 820 ASP cc_start: 0.8415 (t70) cc_final: 0.8110 (t70) REVERT: D 132 MET cc_start: 0.8594 (mmp) cc_final: 0.8352 (mmt) REVERT: D 478 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8993 (tt) REVERT: D 493 THR cc_start: 0.9109 (OUTLIER) cc_final: 0.8751 (p) REVERT: D 562 MET cc_start: 0.9019 (tmm) cc_final: 0.8771 (tmm) REVERT: D 565 MET cc_start: 0.8337 (tmm) cc_final: 0.7516 (tmm) REVERT: D 706 MET cc_start: 0.8312 (tpp) cc_final: 0.7776 (tpp) outliers start: 69 outliers final: 41 residues processed: 250 average time/residue: 0.1116 time to fit residues: 49.9849 Evaluate side-chains 236 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 190 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 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 508 MET 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 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 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 508 MET 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 663 VAL 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: 5.9990 chunk 40 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 204 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 310 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 213 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 HIS ** A 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** 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 = 0.3540 r_free = 0.3540 target = 0.089583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.067032 restraints weight = 80062.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.067394 restraints weight = 46989.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.068013 restraints weight = 35103.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.068320 restraints weight = 32040.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.068448 restraints weight = 28388.668| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 23384 Z= 0.209 Angle : 0.671 12.071 32090 Z= 0.352 Chirality : 0.046 0.374 3916 Planarity : 0.005 0.060 4072 Dihedral : 6.202 51.410 3321 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.08 % Favored : 89.92 % Rotamer: Outliers : 4.79 % Allowed : 20.05 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -2.32 (0.15), residues: 3144 helix: 0.16 (0.14), residues: 1242 sheet: -2.58 (0.24), residues: 396 loop : -2.80 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 544 TYR 0.017 0.001 TYR D 282 PHE 0.022 0.002 PHE D 653 TRP 0.011 0.001 TRP D 772 HIS 0.006 0.001 HIS C 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.21 (23356) covalent geometry : angle 0.66845 / 0.35 (32022) SS BOND : bond 0.00431 / 0.29 ( 16) SS BOND : angle 1.59584 / 1.21 ( 32) hydrogen bonds : bond 0.04514 / 3.17 ( 1038) hydrogen bonds : angle 5.14392 / 3.68 ( 2946) link_BETA1-4 : bond 0.00219 / 0.11 ( 2) link_BETA1-4 : angle 1.32380 / 0.63 ( 6) link_NAG-ASN : bond 0.00272 / 0.20 ( 10) link_NAG-ASN : angle 0.99910 / 0.61 ( 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 301 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 196 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 628 MET cc_start: 0.8281 (tmm) cc_final: 0.7817 (tmm) REVERT: A 683 GLU cc_start: 0.5835 (pp20) cc_final: 0.4934 (mp0) REVERT: A 820 ASP cc_start: 0.8421 (t70) cc_final: 0.8096 (t70) REVERT: B 478 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9124 (tt) REVERT: B 493 THR cc_start: 0.9032 (OUTLIER) cc_final: 0.8723 (p) REVERT: B 551 LEU cc_start: 0.9311 (mt) cc_final: 0.9082 (mt) REVERT: B 561 MET cc_start: 0.8496 (mtp) cc_final: 0.8216 (mtp) REVERT: B 565 MET cc_start: 0.8616 (tmm) cc_final: 0.8139 (tmm) REVERT: B 654 MET cc_start: 0.8494 (tpp) cc_final: 0.8275 (ttt) REVERT: B 706 MET cc_start: 0.8363 (tpp) cc_final: 0.7665 (tpp) REVERT: C 414 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8753 (pp30) REVERT: C 480 CYS cc_start: 0.8389 (p) cc_final: 0.8069 (p) REVERT: C 628 MET cc_start: 0.8164 (tmm) cc_final: 0.7836 (tmm) REVERT: C 820 ASP cc_start: 0.8450 (t70) cc_final: 0.8122 (t70) REVERT: D 478 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9064 (tt) REVERT: D 493 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8757 (p) REVERT: D 562 MET cc_start: 0.9031 (tmm) cc_final: 0.8767 (tmm) REVERT: D 565 MET cc_start: 0.8313 (tmm) cc_final: 0.7595 (tmm) REVERT: D 706 MET cc_start: 0.8475 (tpp) cc_final: 0.7863 (tpp) outliers start: 105 outliers final: 68 residues processed: 282 average time/residue: 0.1148 time to fit residues: 57.2225 Evaluate side-chains 262 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 189 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 167 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 589 LEU Chi-restraints excluded: chain A residue 656 VAL 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 819 CYS Chi-restraints excluded: chain A residue 822 ARG 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 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 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 663 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 736 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 167 VAL Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 414 GLN 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 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 722 THR Chi-restraints excluded: chain C residue 727 MET Chi-restraints excluded: chain C residue 794 SER 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 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 695 ILE Chi-restraints excluded: chain D residue 736 LEU 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: 10.0000 chunk 178 optimal weight: 20.0000 chunk 304 optimal weight: 8.9990 chunk 262 optimal weight: 0.7980 chunk 174 optimal weight: 9.9990 chunk 151 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 252 optimal weight: 10.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 824 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 95 GLN D 697 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.088879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.066187 restraints weight = 80171.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.066652 restraints weight = 48641.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.067139 restraints weight = 36393.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.067366 restraints weight = 33211.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.067525 restraints weight = 29921.662| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 23384 Z= 0.255 Angle : 0.700 13.240 32090 Z= 0.368 Chirality : 0.046 0.386 3916 Planarity : 0.005 0.060 4072 Dihedral : 6.248 51.838 3319 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 5.20 % Allowed : 21.10 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.13 % 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: -2.28 (0.15), residues: 3144 helix: 0.23 (0.14), residues: 1240 sheet: -2.63 (0.24), residues: 406 loop : -2.77 (0.15), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 693 TYR 0.017 0.002 TYR D 282 PHE 0.027 0.002 PHE B 653 TRP 0.014 0.001 TRP B 635 HIS 0.006 0.001 HIS C 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.25 (23356) covalent geometry : angle 0.69776 / 0.37 (32022) SS BOND : bond 0.00557 / 0.35 ( 16) SS BOND : angle 1.72936 / 1.31 ( 32) hydrogen bonds : bond 0.04658 / 3.27 ( 1038) hydrogen bonds : angle 5.20861 / 3.73 ( 2946) link_BETA1-4 : bond 0.00243 / 0.13 ( 2) link_BETA1-4 : angle 1.28552 / 0.61 ( 6) link_NAG-ASN : bond 0.00326 / 0.23 ( 10) link_NAG-ASN : angle 1.13254 / 0.69 ( 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 310 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 196 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: A 628 MET cc_start: 0.8356 (tmm) cc_final: 0.7978 (tmm) REVERT: A 820 ASP cc_start: 0.8541 (t70) cc_final: 0.8281 (t0) REVERT: B 478 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9161 (tt) REVERT: B 493 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8659 (p) REVERT: B 565 MET cc_start: 0.8690 (tmm) cc_final: 0.8156 (tmm) REVERT: B 706 MET cc_start: 0.8444 (tpp) cc_final: 0.7774 (tpp) REVERT: C 480 CYS cc_start: 0.8532 (p) cc_final: 0.8228 (p) REVERT: C 628 MET cc_start: 0.8295 (tmm) cc_final: 0.7901 (tmm) REVERT: C 820 ASP cc_start: 0.8492 (t70) cc_final: 0.8263 (t0) REVERT: D 478 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9105 (tt) REVERT: D 493 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8685 (p) REVERT: D 562 MET cc_start: 0.9014 (tmm) cc_final: 0.8716 (tmm) REVERT: D 565 MET cc_start: 0.8434 (tmm) cc_final: 0.7679 (tmm) REVERT: D 706 MET cc_start: 0.8562 (tpp) cc_final: 0.8060 (tpp) outliers start: 114 outliers final: 89 residues processed: 286 average time/residue: 0.1112 time to fit residues: 56.7622 Evaluate side-chains 283 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 190 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL 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 167 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 589 LEU Chi-restraints excluded: chain A residue 656 VAL 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 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 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 205 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 282 TYR Chi-restraints excluded: chain B residue 406 LEU 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 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 663 VAL Chi-restraints excluded: chain B residue 685 THR 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 C residue 32 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 167 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 589 LEU Chi-restraints excluded: chain C residue 634 VAL 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 722 THR Chi-restraints excluded: chain C residue 727 MET Chi-restraints excluded: chain C residue 742 VAL 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 406 LEU 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 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 663 VAL Chi-restraints excluded: chain D residue 685 THR 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 825 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 102 optimal weight: 20.0000 chunk 153 optimal weight: 8.9990 chunk 217 optimal weight: 0.5980 chunk 254 optimal weight: 4.9990 chunk 216 optimal weight: 0.9990 chunk 241 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 283 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 234 optimal weight: 6.9990 chunk 258 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 671 ASN A 824 ASN C 671 ASN ** C 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.092434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.070038 restraints weight = 78939.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.070583 restraints weight = 45484.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.071327 restraints weight = 33384.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.071614 restraints weight = 29699.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.071708 restraints weight = 26727.945| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 23384 Z= 0.115 Angle : 0.609 13.733 32090 Z= 0.316 Chirality : 0.045 0.358 3916 Planarity : 0.004 0.057 4072 Dihedral : 5.812 58.494 3319 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 4.06 % Allowed : 22.33 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -1.78 (0.15), residues: 3144 helix: 0.60 (0.15), residues: 1246 sheet: -2.40 (0.24), residues: 416 loop : -2.44 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 693 TYR 0.019 0.001 TYR B 282 PHE 0.026 0.001 PHE B 653 TRP 0.013 0.001 TRP B 635 HIS 0.003 0.001 HIS C 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (23356) covalent geometry : angle 0.60715 / 0.32 (32022) SS BOND : bond 0.00534 / 0.28 ( 16) SS BOND : angle 1.63483 / 1.23 ( 32) hydrogen bonds : bond 0.03702 / 2.58 ( 1038) hydrogen bonds : angle 4.71628 / 3.39 ( 2946) link_BETA1-4 : bond 0.00625 / 0.32 ( 2) link_BETA1-4 : angle 0.97680 / 0.48 ( 6) link_NAG-ASN : bond 0.00131 / 0.09 ( 10) link_NAG-ASN : angle 0.89074 / 0.57 ( 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 301 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 212 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 292 LEU cc_start: 0.8655 (tp) cc_final: 0.8335 (tt) REVERT: A 549 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: A 628 MET cc_start: 0.8144 (tmm) cc_final: 0.7785 (tmm) REVERT: B 157 MET cc_start: 0.8012 (ttt) cc_final: 0.7697 (tmm) REVERT: B 478 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.8901 (tt) REVERT: B 493 THR cc_start: 0.9003 (OUTLIER) cc_final: 0.8653 (p) REVERT: B 561 MET cc_start: 0.8636 (mtp) cc_final: 0.8203 (mtp) REVERT: B 565 MET cc_start: 0.8593 (tmm) cc_final: 0.8141 (tmm) REVERT: B 630 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8845 (mm) REVERT: C 292 LEU cc_start: 0.8662 (tp) cc_final: 0.8349 (tt) REVERT: C 480 CYS cc_start: 0.8481 (p) cc_final: 0.8066 (p) REVERT: C 549 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7532 (mp0) REVERT: C 628 MET cc_start: 0.8101 (tmm) cc_final: 0.7707 (tmm) REVERT: D 493 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8676 (p) REVERT: D 562 MET cc_start: 0.9038 (tmm) cc_final: 0.8734 (tmm) REVERT: D 565 MET cc_start: 0.8356 (tmm) cc_final: 0.7636 (tmm) REVERT: D 630 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8873 (mm) REVERT: D 706 MET cc_start: 0.8553 (tpp) cc_final: 0.8246 (tpp) outliers start: 89 outliers final: 55 residues processed: 282 average time/residue: 0.1136 time to fit residues: 57.2902 Evaluate side-chains 262 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 200 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 218 PHE 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 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 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 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 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 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 419 LEU 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 700 PHE 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 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 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 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: 0.0870 chunk 129 optimal weight: 0.9990 chunk 312 optimal weight: 20.0000 chunk 137 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 263 optimal weight: 30.0000 chunk 274 optimal weight: 9.9990 chunk 121 optimal weight: 0.9990 chunk 31 optimal weight: 0.0070 chunk 152 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 ASN A 498 HIS A 824 ASN C 824 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.093709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.071487 restraints weight = 78812.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.072103 restraints weight = 44785.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.072799 restraints weight = 33073.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.072996 restraints weight = 30478.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.073125 restraints weight = 26857.039| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 23384 Z= 0.107 Angle : 0.590 13.911 32090 Z= 0.303 Chirality : 0.044 0.392 3916 Planarity : 0.004 0.055 4072 Dihedral : 5.437 52.762 3318 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.69 % Allowed : 23.15 % Favored : 73.15 % 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: -1.49 (0.15), residues: 3144 helix: 0.74 (0.15), residues: 1260 sheet: -2.09 (0.25), residues: 416 loop : -2.25 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 233 TYR 0.018 0.001 TYR D 282 PHE 0.025 0.001 PHE B 653 TRP 0.012 0.001 TRP B 197 HIS 0.003 0.001 HIS C 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (23356) covalent geometry : angle 0.58763 / 0.30 (32022) SS BOND : bond 0.00360 / 0.22 ( 16) SS BOND : angle 1.51758 / 1.12 ( 32) hydrogen bonds : bond 0.03443 / 2.39 ( 1038) hydrogen bonds : angle 4.52854 / 3.25 ( 2946) link_BETA1-4 : bond 0.00549 / 0.29 ( 2) link_BETA1-4 : angle 1.01057 / 0.49 ( 6) link_NAG-ASN : bond 0.00162 / 0.12 ( 10) link_NAG-ASN : angle 0.81546 / 0.53 ( 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 301 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 220 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 628 MET cc_start: 0.8091 (tmm) cc_final: 0.7688 (tmm) REVERT: A 682 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7643 (mp0) REVERT: A 698 ASP cc_start: 0.8324 (m-30) cc_final: 0.7860 (t0) REVERT: B 493 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8606 (p) REVERT: B 561 MET cc_start: 0.8737 (mtp) cc_final: 0.8302 (mtp) REVERT: B 565 MET cc_start: 0.8582 (tmm) cc_final: 0.8211 (tmm) REVERT: B 630 ILE cc_start: 0.9304 (OUTLIER) cc_final: 0.9011 (mm) REVERT: B 706 MET cc_start: 0.7909 (mmm) cc_final: 0.7509 (tpt) REVERT: C 480 CYS cc_start: 0.8409 (p) cc_final: 0.7977 (p) REVERT: C 628 MET cc_start: 0.8076 (tmm) cc_final: 0.7666 (tmm) REVERT: D 132 MET cc_start: 0.8453 (mmp) cc_final: 0.8133 (mmp) REVERT: D 161 MET cc_start: 0.8658 (ttp) cc_final: 0.8391 (ttm) REVERT: D 478 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.8965 (tt) REVERT: D 493 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8615 (p) REVERT: D 562 MET cc_start: 0.9094 (tmm) cc_final: 0.8755 (tmm) REVERT: D 565 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7730 (tmm) REVERT: D 630 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8802 (mm) REVERT: D 706 MET cc_start: 0.8552 (tpp) cc_final: 0.8249 (tpp) REVERT: D 831 LEU cc_start: 0.8426 (pp) cc_final: 0.8195 (tt) outliers start: 81 outliers final: 58 residues processed: 284 average time/residue: 0.1113 time to fit residues: 56.6622 Evaluate side-chains 267 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 203 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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 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 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 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 493 THR 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 630 ILE Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain C residue 32 VAL 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 548 ILE 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 777 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 54 optimal weight: 1.9990 chunk 287 optimal weight: 0.4980 chunk 64 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 113 optimal weight: 8.9990 chunk 150 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 217 optimal weight: 0.9980 chunk 240 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 47 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 = 0.3611 r_free = 0.3611 target = 0.093389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.070986 restraints weight = 78482.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.071592 restraints weight = 45223.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.072230 restraints weight = 33123.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.072528 restraints weight = 28773.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.072645 restraints weight = 26690.519| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23384 Z= 0.116 Angle : 0.608 14.777 32090 Z= 0.309 Chirality : 0.044 0.421 3916 Planarity : 0.004 0.057 4072 Dihedral : 5.329 46.890 3318 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 3.83 % Allowed : 23.56 % Favored : 72.61 % 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: -1.39 (0.15), residues: 3144 helix: 0.79 (0.15), residues: 1276 sheet: -1.98 (0.25), residues: 416 loop : -2.21 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 233 TYR 0.018 0.001 TYR D 282 PHE 0.029 0.001 PHE B 653 TRP 0.009 0.001 TRP B 635 HIS 0.003 0.001 HIS C 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (23356) covalent geometry : angle 0.60580 / 0.31 (32022) SS BOND : bond 0.00304 / 0.21 ( 16) SS BOND : angle 1.48853 / 1.09 ( 32) hydrogen bonds : bond 0.03477 / 2.42 ( 1038) hydrogen bonds : angle 4.47563 / 3.21 ( 2946) link_BETA1-4 : bond 0.00289 / 0.15 ( 2) link_BETA1-4 : angle 0.93313 / 0.44 ( 6) link_NAG-ASN : bond 0.00183 / 0.13 ( 10) link_NAG-ASN : angle 0.78143 / 0.51 ( 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: 84 poor density : 212 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: A 480 CYS cc_start: 0.8318 (p) cc_final: 0.7921 (p) REVERT: A 628 MET cc_start: 0.8125 (tmm) cc_final: 0.7745 (tmm) REVERT: A 682 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7626 (mp0) REVERT: A 698 ASP cc_start: 0.8310 (m-30) cc_final: 0.7865 (t0) REVERT: B 478 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9010 (tt) REVERT: B 493 THR cc_start: 0.8920 (OUTLIER) cc_final: 0.8582 (p) REVERT: B 561 MET cc_start: 0.8740 (mtp) cc_final: 0.8309 (mtp) REVERT: B 565 MET cc_start: 0.8626 (tmm) cc_final: 0.8255 (tmm) REVERT: B 630 ILE cc_start: 0.9327 (OUTLIER) cc_final: 0.9039 (mm) REVERT: B 706 MET cc_start: 0.7996 (mmm) cc_final: 0.7554 (tpt) REVERT: C 480 CYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8011 (p) REVERT: C 628 MET cc_start: 0.8057 (tmm) cc_final: 0.7657 (tmm) REVERT: C 820 ASP cc_start: 0.8439 (t0) cc_final: 0.8088 (t0) REVERT: D 478 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9087 (tt) REVERT: D 493 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8615 (p) REVERT: D 562 MET cc_start: 0.9123 (tmm) cc_final: 0.8762 (tmm) REVERT: D 565 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.7784 (tmm) REVERT: D 630 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8920 (mm) REVERT: D 706 MET cc_start: 0.8632 (tpp) cc_final: 0.8235 (tpp) REVERT: D 831 LEU cc_start: 0.8428 (pp) cc_final: 0.8195 (tt) outliers start: 84 outliers final: 62 residues processed: 280 average time/residue: 0.1112 time to fit residues: 55.1521 Evaluate side-chains 270 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 200 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL 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 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 777 SER Chi-restraints excluded: chain A residue 794 SER 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 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 510 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 554 PHE 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 750 THR Chi-restraints excluded: chain C residue 32 VAL 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 480 CYS Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 548 ILE 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 777 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 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 777 ASP 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: 0.8980 chunk 270 optimal weight: 8.9990 chunk 234 optimal weight: 0.8980 chunk 259 optimal weight: 4.9990 chunk 298 optimal weight: 0.9990 chunk 265 optimal weight: 0.2980 chunk 201 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 278 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 GLN B 95 GLN B 153 GLN B 697 ASN C 217 GLN C 498 HIS D 95 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.094256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.071864 restraints weight = 79314.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.072524 restraints weight = 45643.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.073137 restraints weight = 33636.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.073679 restraints weight = 29065.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.073709 restraints weight = 26595.253| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 23384 Z= 0.107 Angle : 0.604 14.649 32090 Z= 0.305 Chirality : 0.044 0.415 3916 Planarity : 0.004 0.057 4072 Dihedral : 5.107 40.929 3318 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.65 % Allowed : 24.07 % Favored : 72.29 % 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: -1.24 (0.15), residues: 3144 helix: 0.88 (0.15), residues: 1276 sheet: -1.82 (0.25), residues: 412 loop : -2.13 (0.16), residues: 1456 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 0.029 0.001 PHE B 653 TRP 0.010 0.001 TRP D 166 HIS 0.003 0.000 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (23356) covalent geometry : angle 0.60220 / 0.30 (32022) SS BOND : bond 0.00311 / 0.21 ( 16) SS BOND : angle 1.39195 / 1.02 ( 32) hydrogen bonds : bond 0.03340 / 2.32 ( 1038) hydrogen bonds : angle 4.42237 / 3.17 ( 2946) link_BETA1-4 : bond 0.00291 / 0.15 ( 2) link_BETA1-4 : angle 0.89882 / 0.43 ( 6) link_NAG-ASN : bond 0.00190 / 0.14 ( 10) link_NAG-ASN : angle 0.76168 / 0.50 ( 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 292 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 212 time to evaluate : 0.882 Fit side-chains REVERT: A 480 CYS cc_start: 0.8318 (p) cc_final: 0.7840 (p) REVERT: A 628 MET cc_start: 0.8108 (tmm) cc_final: 0.7726 (tmm) REVERT: A 698 ASP cc_start: 0.8183 (m-30) cc_final: 0.7851 (t0) REVERT: B 478 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.8983 (tt) REVERT: B 493 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8588 (p) REVERT: B 561 MET cc_start: 0.8702 (mtp) cc_final: 0.8375 (mtp) REVERT: B 565 MET cc_start: 0.8681 (tmm) cc_final: 0.8317 (tmm) REVERT: B 630 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.9029 (mm) REVERT: B 706 MET cc_start: 0.8011 (mmm) cc_final: 0.7623 (tpt) REVERT: C 480 CYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8059 (p) REVERT: C 628 MET cc_start: 0.8041 (tmm) cc_final: 0.7620 (tmm) REVERT: C 698 ASP cc_start: 0.8240 (m-30) cc_final: 0.7979 (t0) REVERT: C 820 ASP cc_start: 0.8400 (t0) cc_final: 0.8052 (t0) REVERT: D 478 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9094 (tt) REVERT: D 493 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8587 (p) REVERT: D 561 MET cc_start: 0.8622 (mtp) cc_final: 0.8270 (mtp) REVERT: D 562 MET cc_start: 0.9127 (tmm) cc_final: 0.8759 (tmm) REVERT: D 565 MET cc_start: 0.8533 (tmm) cc_final: 0.7780 (tmm) REVERT: D 630 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8933 (mm) REVERT: D 706 MET cc_start: 0.8628 (tpp) cc_final: 0.8262 (tpp) REVERT: D 831 LEU cc_start: 0.8417 (pp) cc_final: 0.8153 (tt) outliers start: 80 outliers final: 61 residues processed: 274 average time/residue: 0.1184 time to fit residues: 57.3618 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 : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL 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 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 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 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 510 VAL Chi-restraints excluded: chain B residue 554 PHE 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 C residue 32 VAL 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 480 CYS 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 777 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 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 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 777 ASP 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: 0.1980 chunk 254 optimal weight: 7.9990 chunk 128 optimal weight: 6.9990 chunk 265 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 12 optimal weight: 0.0570 overall best weight: 1.8504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.093345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.071055 restraints weight = 79069.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.071434 restraints weight = 47010.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.072209 restraints weight = 34644.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.072692 restraints weight = 29614.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.072699 restraints weight = 26758.857| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23384 Z= 0.131 Angle : 0.621 15.651 32090 Z= 0.314 Chirality : 0.044 0.426 3916 Planarity : 0.004 0.058 4072 Dihedral : 5.050 37.245 3318 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.33 % Allowed : 24.38 % Favored : 72.29 % 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: -1.21 (0.15), residues: 3144 helix: 0.90 (0.15), residues: 1280 sheet: -1.80 (0.25), residues: 412 loop : -2.12 (0.16), residues: 1452 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 0.030 0.001 PHE D 653 TRP 0.011 0.001 TRP D 166 HIS 0.002 0.001 HIS C 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (23356) covalent geometry : angle 0.61946 / 0.31 (32022) SS BOND : bond 0.00330 / 0.22 ( 16) SS BOND : angle 1.44323 / 1.04 ( 32) hydrogen bonds : bond 0.03494 / 2.44 ( 1038) hydrogen bonds : angle 4.46580 / 3.20 ( 2946) link_BETA1-4 : bond 0.00240 / 0.12 ( 2) link_BETA1-4 : angle 0.97832 / 0.45 ( 6) link_NAG-ASN : bond 0.00203 / 0.15 ( 10) link_NAG-ASN : angle 0.78399 / 0.50 ( 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 280 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 207 time to evaluate : 0.806 Fit side-chains REVERT: A 480 CYS cc_start: 0.8476 (p) cc_final: 0.8007 (p) REVERT: A 628 MET cc_start: 0.8151 (tmm) cc_final: 0.7767 (tmm) REVERT: A 698 ASP cc_start: 0.8151 (m-30) cc_final: 0.7832 (t0) REVERT: B 478 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9140 (tt) REVERT: B 493 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8595 (p) REVERT: B 561 MET cc_start: 0.8720 (mtp) cc_final: 0.8393 (mtp) REVERT: B 565 MET cc_start: 0.8683 (tmm) cc_final: 0.8301 (tmm) REVERT: B 706 MET cc_start: 0.8043 (mmm) cc_final: 0.7651 (tpt) REVERT: C 480 CYS cc_start: 0.8490 (p) cc_final: 0.8067 (p) REVERT: C 628 MET cc_start: 0.8081 (tmm) cc_final: 0.7671 (tmm) REVERT: C 698 ASP cc_start: 0.8224 (m-30) cc_final: 0.7970 (t0) REVERT: C 820 ASP cc_start: 0.8363 (t0) cc_final: 0.8007 (t0) REVERT: D 478 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9144 (tt) REVERT: D 493 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8564 (p) REVERT: D 561 MET cc_start: 0.8589 (mtp) cc_final: 0.8252 (mtp) REVERT: D 562 MET cc_start: 0.9143 (tmm) cc_final: 0.8796 (tmm) REVERT: D 565 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.7801 (tmm) REVERT: D 630 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8949 (mm) REVERT: D 706 MET cc_start: 0.8664 (tpp) cc_final: 0.8290 (tpp) REVERT: D 789 MET cc_start: 0.8702 (mmm) cc_final: 0.8498 (tpp) REVERT: D 831 LEU cc_start: 0.8424 (pp) cc_final: 0.8209 (tt) outliers start: 73 outliers final: 62 residues processed: 264 average time/residue: 0.1108 time to fit residues: 52.0754 Evaluate side-chains 274 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 206 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL 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 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 777 SER 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 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 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 718 LEU Chi-restraints excluded: chain C residue 32 VAL 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 777 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 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 663 VAL 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: 1.9990 chunk 131 optimal weight: 8.9990 chunk 288 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 193 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.093579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.071209 restraints weight = 79200.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.071897 restraints weight = 45605.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.072496 restraints weight = 33387.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.072850 restraints weight = 28886.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.072943 restraints weight = 26729.923| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23384 Z= 0.127 Angle : 0.616 15.923 32090 Z= 0.311 Chirality : 0.044 0.406 3916 Planarity : 0.004 0.057 4072 Dihedral : 4.992 33.683 3318 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.37 % Allowed : 24.25 % Favored : 72.38 % 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: -1.15 (0.15), residues: 3144 helix: 0.94 (0.15), residues: 1278 sheet: -1.66 (0.26), residues: 400 loop : -2.12 (0.16), residues: 1466 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 0.032 0.001 PHE B 653 TRP 0.011 0.001 TRP C 629 HIS 0.002 0.001 HIS C 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (23356) covalent geometry : angle 0.61498 / 0.31 (32022) SS BOND : bond 0.00318 / 0.21 ( 16) SS BOND : angle 1.38571 / 1.01 ( 32) hydrogen bonds : bond 0.03455 / 2.42 ( 1038) hydrogen bonds : angle 4.45560 / 3.19 ( 2946) link_BETA1-4 : bond 0.00280 / 0.14 ( 2) link_BETA1-4 : angle 0.94171 / 0.44 ( 6) link_NAG-ASN : bond 0.00199 / 0.14 ( 10) link_NAG-ASN : angle 0.79898 / 0.51 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3277.16 seconds wall clock time: 57 minutes 39.37 seconds (3459.37 seconds total)