Starting phenix.real_space_refine on Mon Oct 26 08:43:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wht_21675/10_2026/6wht_21675.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wht_21675/10_2026/6wht_21675.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6wht_21675/10_2026/6wht_21675.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wht_21675/10_2026/6wht_21675.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wht_21675/10_2026/6wht_21675.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wht_21675/10_2026/6wht_21675.map" model { file = "/net/cci-nas-00/data/ceres_data/6wht_21675/10_2026/6wht_21675.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wht_21675/10_2026/6wht_21675.cif" } resolution = 4.39 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= 0.012 sd= 0.650 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 74 5.16 5 C 13142 2.51 5 N 3376 2.21 5 O 3940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20532 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 793, 5250 Classifications: {'peptide': 793} Incomplete info: {'truncation_to_alanine': 236} Link IDs: {'PTRANS': 35, 'TRANS': 757} Chain breaks: 4 Unresolved non-hydrogen bonds: 1045 Unresolved non-hydrogen angles: 1265 Unresolved non-hydrogen dihedrals: 898 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ARG:plan': 41, 'HIS:plan': 8, 'GLU:plan': 44, 'GLN:plan1': 20, 'PHE:plan': 9, 'ASN:plan1': 15, 'TYR:plan': 6, 'ASP:plan': 19, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 726 Chain: "B" Number of atoms: 4960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 4960 Classifications: {'peptide': 748} Incomplete info: {'truncation_to_alanine': 221} Link IDs: {'PTRANS': 27, 'TRANS': 720} Chain breaks: 6 Unresolved non-hydrogen bonds: 977 Unresolved non-hydrogen angles: 1186 Unresolved non-hydrogen dihedrals: 861 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLU:plan': 31, 'ASP:plan': 22, 'PHE:plan': 20, 'HIS:plan': 7, 'ARG:plan': 20, 'GLN:plan1': 17, 'TYR:plan': 13, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 619 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, D, F Time building chain proxies: 6.83, per 1000 atoms: 0.33 Number of scatterers: 20532 At special positions: 0 Unit cell: (137, 152.07, 183.58, 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 74 16.00 O 3940 8.00 N 3376 7.00 C 13142 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=2.03 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.03 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.04 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.04 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 329 " distance=2.03 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 476 " distance=2.04 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.03 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.04 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 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 A1003 " - " ASN A 224 " " NAG B 901 " - " ASN B 542 " " NAG C1003 " - " ASN C 224 " " NAG D 901 " - " ASN D 542 " " NAG E 1 " - " ASN A 389 " " NAG F 1 " - " ASN C 389 " Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 1.2 seconds 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5752 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 36 sheets defined 45.0% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 70 through 85 removed outlier: 3.542A pdb=" N SER A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.532A pdb=" N SER A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 147 through 159 removed outlier: 4.223A pdb=" N TRP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 184 Processing helix chain 'A' and resid 225 through 233 removed outlier: 3.532A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 259 Processing helix chain 'A' and resid 276 through 283 Processing helix chain 'A' and resid 298 through 318 removed outlier: 3.609A pdb=" N SER A 303 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU A 318 " --> pdb=" O HIS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 349 Processing helix chain 'A' and resid 478 through 492 Processing helix chain 'A' and resid 520 through 529 removed outlier: 3.697A pdb=" N GLY A 524 " --> pdb=" O ASN A 520 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 547 Processing helix chain 'A' and resid 580 through 603 removed outlier: 3.525A pdb=" N TRP A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY A 588 " --> pdb=" O TRP A 584 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A 603 " --> pdb=" O TYR A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 637 removed outlier: 3.888A pdb=" N PHE A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 631 " --> pdb=" O ALA A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 676 removed outlier: 5.819A pdb=" N MET A 655 " --> pdb=" O ARG A 651 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TRP A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 695 Processing helix chain 'A' and resid 708 through 717 removed outlier: 3.618A pdb=" N ILE A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 728 Processing helix chain 'A' and resid 734 through 744 removed outlier: 3.775A pdb=" N ALA A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 765 removed outlier: 5.073A pdb=" N PHE A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 803 removed outlier: 3.546A pdb=" N SER A 794 " --> pdb=" O LYS A 790 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 795 " --> pdb=" O GLN A 791 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER A 796 " --> pdb=" O GLN A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 830 through 861 removed outlier: 3.630A pdb=" N MET A 834 " --> pdb=" O THR A 830 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL A 837 " --> pdb=" O ASN A 833 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS A 861 " --> pdb=" O ALA A 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 57 removed outlier: 4.129A pdb=" N HIS B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 Processing helix chain 'B' and resid 107 through 120 removed outlier: 3.785A pdb=" N GLN B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 149 through 165 Processing helix chain 'B' and resid 178 through 192 Processing helix chain 'B' and resid 214 through 223 Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 265 through 269 Processing helix chain 'B' and resid 289 through 312 removed outlier: 5.388A pdb=" N ASP B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ALA B 298 " --> pdb=" O ARG B 294 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR B 301 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ALA B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA B 304 " --> pdb=" O ILE B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 328 removed outlier: 3.943A pdb=" N HIS B 325 " --> pdb=" O TYR B 322 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG B 328 " --> pdb=" O HIS B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 341 removed outlier: 3.637A pdb=" N ARG B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN B 341 " --> pdb=" O ARG B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 470 removed outlier: 3.708A pdb=" N LYS B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 516 through 521 Processing helix chain 'B' and resid 556 through 568 Processing helix chain 'B' and resid 568 through 579 removed outlier: 4.254A pdb=" N VAL B 572 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR B 579 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 615 removed outlier: 3.752A pdb=" N PHE B 614 " --> pdb=" O TRP B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 654 removed outlier: 4.672A pdb=" N SER B 633 " --> pdb=" O LYS B 629 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TRP B 635 " --> pdb=" O MET B 631 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 673 through 678 Processing helix chain 'B' and resid 690 through 699 removed outlier: 4.127A pdb=" N ASN B 694 " --> pdb=" O SER B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 707 Processing helix chain 'B' and resid 708 through 710 No H-bonds generated for 'chain 'B' and resid 708 through 710' Processing helix chain 'B' and resid 714 through 724 Processing helix chain 'B' and resid 733 through 740 Processing helix chain 'B' and resid 741 through 742 No H-bonds generated for 'chain 'B' and resid 741 through 742' Processing helix chain 'B' and resid 743 through 748 Processing helix chain 'B' and resid 772 through 785 Processing helix chain 'B' and resid 787 through 797 Processing helix chain 'B' and resid 818 through 837 removed outlier: 3.705A pdb=" N PHE B 822 " --> pdb=" O MET B 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 50 Processing helix chain 'C' and resid 70 through 85 removed outlier: 3.542A pdb=" N SER C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.531A pdb=" N SER C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 131 Processing helix chain 'C' and resid 144 through 146 No H-bonds generated for 'chain 'C' and resid 144 through 146' Processing helix chain 'C' and resid 147 through 159 removed outlier: 4.224A pdb=" N TRP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 184 Processing helix chain 'C' and resid 225 through 233 removed outlier: 3.532A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 259 Processing helix chain 'C' and resid 276 through 283 Processing helix chain 'C' and resid 298 through 318 removed outlier: 3.609A pdb=" N SER C 303 " --> pdb=" O SER C 299 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU C 318 " --> pdb=" O HIS C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 349 Processing helix chain 'C' and resid 478 through 492 Processing helix chain 'C' and resid 520 through 529 removed outlier: 3.696A pdb=" N GLY C 524 " --> pdb=" O ASN C 520 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY C 529 " --> pdb=" O GLU C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 547 Processing helix chain 'C' and resid 580 through 603 removed outlier: 3.525A pdb=" N TRP C 584 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY C 588 " --> pdb=" O TRP C 584 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG C 603 " --> pdb=" O TYR C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 637 removed outlier: 3.889A pdb=" N PHE C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER C 631 " --> pdb=" O ALA C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 676 removed outlier: 5.819A pdb=" N MET C 655 " --> pdb=" O ARG C 651 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TRP C 657 " --> pdb=" O LEU C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 695 Processing helix chain 'C' and resid 708 through 717 removed outlier: 3.619A pdb=" N ILE C 712 " --> pdb=" O SER C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 728 Processing helix chain 'C' and resid 734 through 744 removed outlier: 3.775A pdb=" N ALA C 738 " --> pdb=" O SER C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 765 removed outlier: 5.073A pdb=" N PHE C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 803 removed outlier: 3.546A pdb=" N SER C 794 " --> pdb=" O LYS C 790 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU C 795 " --> pdb=" O GLN C 791 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER C 796 " --> pdb=" O GLN C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 814 Processing helix chain 'C' and resid 830 through 861 removed outlier: 3.630A pdb=" N MET C 834 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL C 837 " --> pdb=" O ASN C 833 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS C 861 " --> pdb=" O ALA C 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 57 removed outlier: 4.128A pdb=" N HIS D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 92 Processing helix chain 'D' and resid 107 through 120 removed outlier: 3.784A pdb=" N GLN D 118 " --> pdb=" O PHE D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 149 through 165 Processing helix chain 'D' and resid 178 through 192 Processing helix chain 'D' and resid 214 through 223 Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 265 through 269 Processing helix chain 'D' and resid 289 through 312 removed outlier: 5.388A pdb=" N ASP D 295 " --> pdb=" O ALA D 291 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ALA D 298 " --> pdb=" O ARG D 294 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR D 301 " --> pdb=" O ILE D 297 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ALA D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA D 304 " --> pdb=" O ILE D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 328 removed outlier: 3.943A pdb=" N HIS D 325 " --> pdb=" O TYR D 322 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG D 328 " --> pdb=" O HIS D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 341 removed outlier: 3.636A pdb=" N ARG D 337 " --> pdb=" O ASN D 333 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 470 removed outlier: 3.708A pdb=" N LYS D 470 " --> pdb=" O LYS D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 503 Processing helix chain 'D' and resid 516 through 521 Processing helix chain 'D' and resid 556 through 568 Processing helix chain 'D' and resid 568 through 579 removed outlier: 4.253A pdb=" N VAL D 572 " --> pdb=" O ILE D 568 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR D 579 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 615 removed outlier: 3.751A pdb=" N PHE D 614 " --> pdb=" O TRP D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 654 removed outlier: 4.673A pdb=" N SER D 633 " --> pdb=" O LYS D 629 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TRP D 635 " --> pdb=" O MET D 631 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA D 648 " --> pdb=" O ALA D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 673 through 678 Processing helix chain 'D' and resid 690 through 699 removed outlier: 4.127A pdb=" N ASN D 694 " --> pdb=" O SER D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 707 Processing helix chain 'D' and resid 708 through 710 No H-bonds generated for 'chain 'D' and resid 708 through 710' Processing helix chain 'D' and resid 714 through 724 Processing helix chain 'D' and resid 733 through 740 Processing helix chain 'D' and resid 741 through 742 No H-bonds generated for 'chain 'D' and resid 741 through 742' Processing helix chain 'D' and resid 743 through 748 Processing helix chain 'D' and resid 772 through 785 Processing helix chain 'D' and resid 787 through 797 Processing helix chain 'D' and resid 818 through 837 removed outlier: 3.704A pdb=" N PHE D 822 " --> pdb=" O MET D 818 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 removed outlier: 6.742A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 165 through 166 removed outlier: 7.156A pdb=" N LEU A 165 " --> pdb=" O LEU A 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 239 through 240 removed outlier: 3.506A pdb=" N ILE A 240 " --> pdb=" O VAL A 267 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 288 through 292 removed outlier: 6.161A pdb=" N TYR A 372 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE A 387 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE A 374 " --> pdb=" O VAL A 385 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 360 through 362 Processing sheet with id=AA6, first strand: chain 'A' and resid 494 through 498 removed outlier: 6.295A pdb=" N LEU A 419 " --> pdb=" O GLU A 496 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N HIS A 498 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE A 421 " --> pdb=" O HIS A 498 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET A 533 " --> pdb=" O LYS A 420 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL A 422 " --> pdb=" O MET A 533 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A 549 " --> pdb=" O MET A 783 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 431 through 434 Processing sheet with id=AA8, first strand: chain 'A' and resid 508 through 509 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 751 Processing sheet with id=AB2, first strand: chain 'B' and resid 66 through 72 removed outlier: 3.512A pdb=" N GLU B 69 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU B 41 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ILE B 126 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N PHE B 99 " --> pdb=" O ILE B 126 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 171 through 173 removed outlier: 6.708A pdb=" N ILE B 228 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 278 through 279 Processing sheet with id=AB5, first strand: chain 'B' and resid 378 through 380 Processing sheet with id=AB6, first strand: chain 'B' and resid 408 through 409 removed outlier: 3.524A pdb=" N VAL B 409 " --> pdb=" O MET B 508 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B 765 " --> pdb=" O ALA B 509 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 434 through 435 Processing sheet with id=AB8, first strand: chain 'B' and resid 488 through 489 Processing sheet with id=AB9, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.582A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N ASP B 732 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ILE B 534 " --> pdb=" O ALA B 758 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA B 758 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 64 through 66 removed outlier: 6.742A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 165 through 166 removed outlier: 7.156A pdb=" N LEU C 165 " --> pdb=" O LEU C 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 239 through 240 removed outlier: 3.507A pdb=" N ILE C 240 " --> pdb=" O VAL C 267 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 288 through 292 removed outlier: 6.160A pdb=" N TYR C 372 " --> pdb=" O ILE C 387 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE C 387 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE C 374 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 360 through 362 Processing sheet with id=AC6, first strand: chain 'C' and resid 494 through 498 removed outlier: 6.294A pdb=" N LEU C 419 " --> pdb=" O GLU C 496 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N HIS C 498 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE C 421 " --> pdb=" O HIS C 498 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET C 533 " --> pdb=" O LYS C 420 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL C 422 " --> pdb=" O MET C 533 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU C 549 " --> pdb=" O MET C 783 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 431 through 434 Processing sheet with id=AC8, first strand: chain 'C' and resid 508 through 509 Processing sheet with id=AC9, first strand: chain 'C' and resid 555 through 557 Processing sheet with id=AD1, first strand: chain 'C' and resid 750 through 751 Processing sheet with id=AD2, first strand: chain 'D' and resid 66 through 72 removed outlier: 3.512A pdb=" N GLU D 69 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU D 41 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE D 126 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N PHE D 99 " --> pdb=" O ILE D 126 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 171 through 173 removed outlier: 6.708A pdb=" N ILE D 228 " --> pdb=" O ILE D 257 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 278 through 279 Processing sheet with id=AD5, first strand: chain 'D' and resid 378 through 380 Processing sheet with id=AD6, first strand: chain 'D' and resid 408 through 409 removed outlier: 3.523A pdb=" N VAL D 409 " --> pdb=" O MET D 508 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA D 765 " --> pdb=" O ALA D 509 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 434 through 435 Processing sheet with id=AD8, first strand: chain 'D' and resid 488 through 489 Processing sheet with id=AD9, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.581A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ILE D 534 " --> pdb=" O ALA D 758 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA D 758 " --> pdb=" O ILE D 534 " (cutoff:3.500A) 986 hydrogen bonds defined for protein. 2790 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.01 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6723 1.34 - 1.46: 4937 1.46 - 1.58: 9156 1.58 - 1.70: 0 1.70 - 1.82: 106 Bond restraints: 20922 Sorted by residual: bond pdb=" C ALA A 536 " pdb=" N PRO A 537 " ideal model delta sigma weight residual 1.332 1.300 0.032 1.12e-02 7.97e+03 7.99e+00 bond pdb=" C ALA C 536 " pdb=" N PRO C 537 " ideal model delta sigma weight residual 1.332 1.301 0.031 1.12e-02 7.97e+03 7.84e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.83e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.82e+00 bond pdb=" N GLY A 558 " pdb=" CA GLY A 558 " ideal model delta sigma weight residual 1.458 1.443 0.015 9.20e-03 1.18e+04 2.75e+00 ... (remaining 20917 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 27936 2.08 - 4.15: 836 4.15 - 6.23: 98 6.23 - 8.31: 18 8.31 - 10.39: 6 Bond angle restraints: 28894 Sorted by residual: angle pdb=" C SER D 526 " pdb=" N VAL D 527 " pdb=" CA VAL D 527 " ideal model delta sigma weight residual 122.59 119.55 3.04 7.20e-01 1.93e+00 1.78e+01 angle pdb=" C SER B 526 " pdb=" N VAL B 527 " pdb=" CA VAL B 527 " ideal model delta sigma weight residual 122.59 119.63 2.96 7.20e-01 1.93e+00 1.69e+01 angle pdb=" C SER A 464 " pdb=" CA SER A 464 " pdb=" CB SER A 464 " ideal model delta sigma weight residual 111.20 108.48 2.72 7.10e-01 1.98e+00 1.47e+01 angle pdb=" CA CYS D 321 " pdb=" CB CYS D 321 " pdb=" SG CYS D 321 " ideal model delta sigma weight residual 114.40 123.21 -8.81 2.30e+00 1.89e-01 1.47e+01 angle pdb=" CA CYS B 321 " pdb=" CB CYS B 321 " pdb=" SG CYS B 321 " ideal model delta sigma weight residual 114.40 123.19 -8.79 2.30e+00 1.89e-01 1.46e+01 ... (remaining 28889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 11071 17.21 - 34.42: 821 34.42 - 51.62: 115 51.62 - 68.83: 33 68.83 - 86.04: 4 Dihedral angle restraints: 12044 sinusoidal: 3162 harmonic: 8882 Sorted by residual: dihedral pdb=" CA CYS B 321 " pdb=" C CYS B 321 " pdb=" N TYR B 322 " pdb=" CA TYR B 322 " ideal model delta harmonic sigma weight residual -180.00 -130.67 -49.33 0 5.00e+00 4.00e-02 9.74e+01 dihedral pdb=" CA CYS D 321 " pdb=" C CYS D 321 " pdb=" N TYR D 322 " pdb=" CA TYR D 322 " ideal model delta harmonic sigma weight residual -180.00 -130.70 -49.30 0 5.00e+00 4.00e-02 9.72e+01 dihedral pdb=" CA ARG B 439 " pdb=" C ARG B 439 " pdb=" N ILE B 440 " pdb=" CA ILE B 440 " ideal model delta harmonic sigma weight residual 180.00 131.15 48.85 0 5.00e+00 4.00e-02 9.54e+01 ... (remaining 12041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.223: 3736 0.223 - 0.446: 2 0.446 - 0.669: 0 0.669 - 0.892: 0 0.892 - 1.114: 2 Chirality restraints: 3740 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 -1.29 -1.11 2.00e-02 2.50e+03 3.10e+03 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 -1.29 -1.11 2.00e-02 2.50e+03 3.09e+03 chirality pdb=" CB VAL C 756 " pdb=" CA VAL C 756 " pdb=" CG1 VAL C 756 " pdb=" CG2 VAL C 756 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 3737 not shown) Planarity restraints: 3688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 414 " 0.048 5.00e-02 4.00e+02 7.29e-02 8.50e+00 pdb=" N PRO B 415 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 415 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 415 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 414 " -0.048 5.00e-02 4.00e+02 7.27e-02 8.46e+00 pdb=" N PRO D 415 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO D 415 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 415 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 679 " -0.043 5.00e-02 4.00e+02 6.45e-02 6.66e+00 pdb=" N PRO D 680 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO D 680 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 680 " -0.036 5.00e-02 4.00e+02 ... (remaining 3685 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 288 2.57 - 3.15: 21015 3.15 - 3.73: 32165 3.73 - 4.32: 40631 4.32 - 4.90: 60657 Nonbonded interactions: 154756 Sorted by model distance: nonbonded pdb=" OG1 THR C 446 " pdb=" O GLY C 449 " model vdw 1.983 3.040 nonbonded pdb=" OG1 THR A 446 " pdb=" O GLY A 449 " model vdw 1.983 3.040 nonbonded pdb=" OG SER B 170 " pdb=" O ILE B 227 " model vdw 2.004 3.040 nonbonded pdb=" OG SER D 170 " pdb=" O ILE D 227 " model vdw 2.005 3.040 nonbonded pdb=" OG SER D 34 " pdb=" O VAL D 65 " model vdw 2.047 3.040 ... (remaining 154751 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 21.990 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 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 : 0.006 0.065 20946 Z= 0.328 Angle : 0.874 14.151 28950 Z= 0.490 Chirality : 0.053 1.114 3740 Planarity : 0.006 0.073 3682 Dihedral : 12.853 86.039 6244 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 23.40 Ramachandran Plot: Outliers : 0.33 % Allowed : 17.34 % Favored : 82.33 % Rotamer: Outliers : 0.63 % Allowed : 11.45 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -5.16 (0.12), residues: 3034 helix: -2.83 (0.12), residues: 1140 sheet: -3.98 (0.24), residues: 284 loop : -3.89 (0.14), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 715 TYR 0.031 0.003 TYR D 167 PHE 0.016 0.002 PHE D 822 TRP 0.021 0.002 TRP D 559 HIS 0.008 0.002 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.33 (20922) covalent geometry : angle 0.85162 / 0.49 (28894) SS BOND : bond 0.00555 / 0.35 ( 16) SS BOND : angle 1.85049 / 1.39 ( 32) hydrogen bonds : bond 0.20521 / 14.22 ( 986) hydrogen bonds : angle 7.82973 / 5.64 ( 2790) link_BETA1-4 : bond 0.06466 / 3.24 ( 2) link_BETA1-4 : angle 9.57062 / 4.58 ( 6) link_NAG-ASN : bond 0.00612 / 0.38 ( 6) link_NAG-ASN : angle 5.16403 / 3.78 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 188 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.7179 (mp) cc_final: 0.6860 (mp) REVERT: A 806 MET cc_start: 0.6967 (mmm) cc_final: 0.6741 (tpp) REVERT: C 125 MET cc_start: 0.7313 (mmm) cc_final: 0.6899 (mmm) REVERT: D 782 GLN cc_start: 0.6560 (tp40) cc_final: 0.6119 (tp40) outliers start: 11 outliers final: 6 residues processed: 197 average time/residue: 0.0964 time to fit residues: 34.2486 Evaluate side-chains 159 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 153 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 ASN A 147 GLN B 118 GLN B 159 ASN B 486 HIS B 616 ASN C 50 ASN C 147 GLN ** C 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 ASN D 486 HIS D 616 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.061495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.050677 restraints weight = 162058.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.051680 restraints weight = 108090.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.052400 restraints weight = 80792.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.052916 restraints weight = 65170.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.053138 restraints weight = 55776.314| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20946 Z= 0.189 Angle : 0.740 10.841 28950 Z= 0.393 Chirality : 0.047 0.232 3740 Planarity : 0.005 0.076 3682 Dihedral : 6.580 46.646 3144 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.98 % Favored : 88.83 % Rotamer: Outliers : 0.57 % Allowed : 7.86 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.69 (0.14), residues: 3034 helix: -1.26 (0.13), residues: 1202 sheet: -3.45 (0.24), residues: 308 loop : -3.31 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 774 TYR 0.023 0.002 TYR D 167 PHE 0.017 0.002 PHE B 822 TRP 0.022 0.002 TRP D 166 HIS 0.005 0.001 HIS A 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.19 (20922) covalent geometry : angle 0.72937 / 0.39 (28894) SS BOND : bond 0.00525 / 0.29 ( 16) SS BOND : angle 1.88101 / 1.42 ( 32) hydrogen bonds : bond 0.05845 / 4.16 ( 986) hydrogen bonds : angle 6.00394 / 4.31 ( 2790) link_BETA1-4 : bond 0.01997 / 0.99 ( 2) link_BETA1-4 : angle 0.60886 / 0.28 ( 6) link_NAG-ASN : bond 0.00599 / 0.39 ( 6) link_NAG-ASN : angle 4.60474 / 3.35 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 211 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8917 (mp) cc_final: 0.8466 (mp) REVERT: A 727 MET cc_start: 0.8641 (ptp) cc_final: 0.8297 (ptp) REVERT: A 774 PHE cc_start: 0.7839 (m-80) cc_final: 0.7170 (m-80) REVERT: C 125 MET cc_start: 0.8791 (mmm) cc_final: 0.8419 (mmm) REVERT: D 89 MET cc_start: 0.7257 (mmm) cc_final: 0.6993 (tpt) REVERT: D 358 MET cc_start: 0.7762 (mmp) cc_final: 0.7481 (mmm) outliers start: 10 outliers final: 3 residues processed: 221 average time/residue: 0.1015 time to fit residues: 39.7956 Evaluate side-chains 168 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 165 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: [41, 55, 168, 295, 176, 38, 39, 279, 107, 125, 222] chunk 41 optimal weight: 0.0670 chunk 55 optimal weight: 6.9990 chunk 168 optimal weight: 10.0000 chunk 295 optimal weight: 5.9990 chunk 176 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 279 optimal weight: 0.0070 chunk 107 optimal weight: 9.9990 chunk 125 optimal weight: 0.7980 chunk 222 optimal weight: 5.9990 overall best weight: 1.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 HIS C 392 HIS C 637 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.063208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.052324 restraints weight = 161584.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.053335 restraints weight = 107425.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.054083 restraints weight = 80276.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.054590 restraints weight = 64548.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.054962 restraints weight = 55278.221| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20946 Z= 0.135 Angle : 0.678 10.384 28950 Z= 0.355 Chirality : 0.046 0.243 3740 Planarity : 0.005 0.067 3682 Dihedral : 6.052 45.858 3144 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.85 % Favored : 90.05 % Rotamer: Outliers : 0.11 % Allowed : 6.32 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.74 (0.15), residues: 3034 helix: -0.25 (0.14), residues: 1228 sheet: -2.91 (0.25), residues: 310 loop : -3.02 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 715 TYR 0.034 0.002 TYR A 724 PHE 0.048 0.001 PHE B 241 TRP 0.025 0.001 TRP D 166 HIS 0.004 0.001 HIS A 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (20922) covalent geometry : angle 0.66615 / 0.35 (28894) SS BOND : bond 0.01337 / 0.81 ( 16) SS BOND : angle 1.57361 / 1.11 ( 32) hydrogen bonds : bond 0.04682 / 3.30 ( 986) hydrogen bonds : angle 5.36333 / 3.83 ( 2790) link_BETA1-4 : bond 0.01320 / 0.67 ( 2) link_BETA1-4 : angle 0.95200 / 0.49 ( 6) link_NAG-ASN : bond 0.00609 / 0.39 ( 6) link_NAG-ASN : angle 4.61352 / 3.35 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 201 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8893 (mp) cc_final: 0.8467 (mp) REVERT: A 728 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: B 89 MET cc_start: 0.6962 (tpt) cc_final: 0.6674 (tpt) REVERT: C 165 LEU cc_start: 0.9449 (tp) cc_final: 0.9152 (tp) REVERT: C 671 ASN cc_start: 0.8742 (m-40) cc_final: 0.8088 (t0) outliers start: 2 outliers final: 1 residues processed: 203 average time/residue: 0.0929 time to fit residues: 33.9778 Evaluate side-chains 166 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 164 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: [43, 282, 88, 206, 70, 301, 1, 63, 118, 242, 276] chunk 43 optimal weight: 9.9990 chunk 282 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 206 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 301 optimal weight: 0.9980 chunk 1 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 242 optimal weight: 20.0000 chunk 276 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 HIS A 717 GLN B 336 ASN C 134 HIS D 336 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.063974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.053122 restraints weight = 160982.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.054155 restraints weight = 107091.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.054902 restraints weight = 79707.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.055405 restraints weight = 64252.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.055814 restraints weight = 55224.558| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20946 Z= 0.121 Angle : 0.647 10.182 28950 Z= 0.336 Chirality : 0.045 0.236 3740 Planarity : 0.005 0.065 3682 Dihedral : 5.753 46.712 3144 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.00 % Favored : 90.84 % Rotamer: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.17 (0.15), residues: 3034 helix: 0.32 (0.15), residues: 1222 sheet: -2.65 (0.25), residues: 322 loop : -2.78 (0.16), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 544 TYR 0.020 0.001 TYR A 724 PHE 0.041 0.001 PHE B 241 TRP 0.021 0.001 TRP D 166 HIS 0.004 0.001 HIS A 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (20922) covalent geometry : angle 0.63459 / 0.33 (28894) SS BOND : bond 0.00905 / 0.46 ( 16) SS BOND : angle 1.85987 / 1.36 ( 32) hydrogen bonds : bond 0.04078 / 2.86 ( 986) hydrogen bonds : angle 5.04516 / 3.58 ( 2790) link_BETA1-4 : bond 0.01024 / 0.51 ( 2) link_BETA1-4 : angle 0.97582 / 0.48 ( 6) link_NAG-ASN : bond 0.00585 / 0.38 ( 6) link_NAG-ASN : angle 4.51871 / 3.28 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LEU cc_start: 0.8822 (mp) cc_final: 0.8389 (mp) REVERT: C 165 LEU cc_start: 0.9363 (tp) cc_final: 0.9140 (tp) REVERT: C 522 MET cc_start: 0.9338 (ptp) cc_final: 0.8713 (mpp) REVERT: C 523 MET cc_start: 0.8636 (mmt) cc_final: 0.8237 (tpt) REVERT: C 671 ASN cc_start: 0.8792 (m-40) cc_final: 0.8195 (t0) REVERT: D 89 MET cc_start: 0.7477 (tpt) cc_final: 0.7047 (tpt) REVERT: D 161 MET cc_start: 0.8731 (mmm) cc_final: 0.8529 (mmm) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.1008 time to fit residues: 34.3346 Evaluate side-chains 162 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: [165, 159, 137, 18, 217, 172, 91, 156, 84, 136, 236] chunk 165 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 137 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 217 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 156 optimal weight: 30.0000 chunk 84 optimal weight: 8.9990 chunk 136 optimal weight: 30.0000 chunk 236 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 801 HIS B 336 ASN C 801 HIS D 336 ASN D 649 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.062643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.051767 restraints weight = 161756.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.052780 restraints weight = 107795.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.053498 restraints weight = 80642.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.053992 restraints weight = 65259.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.054402 restraints weight = 56021.111| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20946 Z= 0.183 Angle : 0.673 10.474 28950 Z= 0.352 Chirality : 0.045 0.248 3740 Planarity : 0.005 0.061 3682 Dihedral : 5.828 47.583 3144 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.88 % Favored : 89.02 % Rotamer: Outliers : 0.06 % Allowed : 3.76 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.15), residues: 3034 helix: 0.37 (0.15), residues: 1228 sheet: -2.76 (0.26), residues: 314 loop : -2.71 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 519 TYR 0.023 0.002 TYR B 167 PHE 0.039 0.001 PHE B 241 TRP 0.015 0.002 TRP D 559 HIS 0.008 0.002 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 (20922) covalent geometry : angle 0.66150 / 0.35 (28894) SS BOND : bond 0.01126 / 0.71 ( 16) SS BOND : angle 1.63410 / 1.24 ( 32) hydrogen bonds : bond 0.04263 / 3.00 ( 986) hydrogen bonds : angle 5.11542 / 3.64 ( 2790) link_BETA1-4 : bond 0.00846 / 0.43 ( 2) link_BETA1-4 : angle 1.07264 / 0.56 ( 6) link_NAG-ASN : bond 0.00494 / 0.33 ( 6) link_NAG-ASN : angle 4.58885 / 3.32 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 MET cc_start: 0.9388 (ptp) cc_final: 0.9080 (mpp) REVERT: B 241 PHE cc_start: 0.8804 (m-80) cc_final: 0.8408 (m-10) REVERT: C 523 MET cc_start: 0.8649 (mmt) cc_final: 0.8257 (tpt) REVERT: C 774 PHE cc_start: 0.8041 (m-80) cc_final: 0.7483 (m-80) REVERT: D 161 MET cc_start: 0.8829 (mmm) cc_final: 0.8619 (mmm) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.0983 time to fit residues: 32.1851 Evaluate side-chains 154 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: [280, 253, 161, 243, 61, 238, 15, 102, 134, 98, 109] chunk 280 optimal weight: 5.9990 chunk 253 optimal weight: 20.0000 chunk 161 optimal weight: 8.9990 chunk 243 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 238 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 102 optimal weight: 0.4980 chunk 134 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 118 GLN ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.062170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.051313 restraints weight = 161084.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.052320 restraints weight = 108043.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.053014 restraints weight = 81048.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.053549 restraints weight = 65947.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.053935 restraints weight = 56370.722| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20946 Z= 0.190 Angle : 0.690 10.061 28950 Z= 0.361 Chirality : 0.046 0.269 3740 Planarity : 0.005 0.065 3682 Dihedral : 5.927 49.753 3144 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.74 % Favored : 89.16 % Rotamer: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.15), residues: 3034 helix: 0.38 (0.15), residues: 1226 sheet: -2.80 (0.25), residues: 316 loop : -2.68 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 715 TYR 0.021 0.002 TYR D 167 PHE 0.030 0.002 PHE B 241 TRP 0.022 0.002 TRP A 268 HIS 0.009 0.002 HIS C 592 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.19 (20922) covalent geometry : angle 0.67838 / 0.36 (28894) SS BOND : bond 0.00656 / 0.42 ( 16) SS BOND : angle 1.89351 / 1.45 ( 32) hydrogen bonds : bond 0.04309 / 3.04 ( 986) hydrogen bonds : angle 5.15298 / 3.66 ( 2790) link_BETA1-4 : bond 0.00845 / 0.43 ( 2) link_BETA1-4 : angle 1.10828 / 0.58 ( 6) link_NAG-ASN : bond 0.00483 / 0.32 ( 6) link_NAG-ASN : angle 4.56630 / 3.30 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 MET cc_start: 0.9206 (ptp) cc_final: 0.8883 (mpp) REVERT: C 522 MET cc_start: 0.9299 (ptp) cc_final: 0.8884 (mpp) REVERT: C 523 MET cc_start: 0.8623 (mmt) cc_final: 0.8408 (mmt) REVERT: C 636 LEU cc_start: 0.9410 (mt) cc_final: 0.9010 (tp) REVERT: C 774 PHE cc_start: 0.8139 (m-80) cc_final: 0.7581 (m-80) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.0953 time to fit residues: 30.2634 Evaluate side-chains 157 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: [83, 155, 29, 102, 27, 129, 180, 30, 55, 133, 277] chunk 83 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 102 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 129 optimal weight: 10.0000 chunk 180 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 55 optimal weight: 20.0000 chunk 133 optimal weight: 7.9990 chunk 277 optimal weight: 0.8980 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 717 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.062334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.051433 restraints weight = 161390.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.052454 restraints weight = 108118.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.053147 restraints weight = 80911.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.053692 restraints weight = 65688.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.054075 restraints weight = 56161.082| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20946 Z= 0.181 Angle : 0.686 10.342 28950 Z= 0.358 Chirality : 0.045 0.236 3740 Planarity : 0.005 0.063 3682 Dihedral : 5.923 48.361 3144 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.44 % Favored : 88.53 % Rotamer: Outliers : 0.11 % Allowed : 1.99 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.02 (0.15), residues: 3034 helix: 0.47 (0.15), residues: 1226 sheet: -2.81 (0.25), residues: 330 loop : -2.66 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 743 TYR 0.020 0.002 TYR D 167 PHE 0.019 0.001 PHE C 660 TRP 0.021 0.002 TRP C 268 HIS 0.005 0.001 HIS A 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (20922) covalent geometry : angle 0.67419 / 0.35 (28894) SS BOND : bond 0.00554 / 0.35 ( 16) SS BOND : angle 1.96112 / 1.51 ( 32) hydrogen bonds : bond 0.04210 / 2.98 ( 986) hydrogen bonds : angle 5.08783 / 3.62 ( 2790) link_BETA1-4 : bond 0.00997 / 0.50 ( 2) link_BETA1-4 : angle 1.13705 / 0.59 ( 6) link_NAG-ASN : bond 0.00497 / 0.33 ( 6) link_NAG-ASN : angle 4.53432 / 3.29 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 177 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 MET cc_start: 0.8614 (mtp) cc_final: 0.8339 (mtp) REVERT: A 776 ARG cc_start: 0.8635 (mmm-85) cc_final: 0.8389 (mtp85) REVERT: B 161 MET cc_start: 0.8214 (ptp) cc_final: 0.7978 (ptm) REVERT: C 523 MET cc_start: 0.8712 (mmt) cc_final: 0.8241 (tpt) REVERT: C 774 PHE cc_start: 0.8155 (m-80) cc_final: 0.7630 (m-80) REVERT: D 782 GLN cc_start: 0.8658 (tp40) cc_final: 0.8174 (tp40) outliers start: 2 outliers final: 0 residues processed: 179 average time/residue: 0.0948 time to fit residues: 30.1626 Evaluate side-chains 155 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: [208, 103, 11, 0, 283, 246, 186, 242, 142, 197, 189] chunk 208 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 11 optimal weight: 0.0670 chunk 0 optimal weight: 30.0000 chunk 283 optimal weight: 9.9990 chunk 246 optimal weight: 0.0020 chunk 186 optimal weight: 9.9990 chunk 242 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 chunk 197 optimal weight: 8.9990 chunk 189 optimal weight: 0.0270 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 726 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.062974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.052042 restraints weight = 161017.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.053066 restraints weight = 108199.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.053806 restraints weight = 80965.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.054334 restraints weight = 65357.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.054680 restraints weight = 55927.820| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20946 Z= 0.150 Angle : 0.664 15.071 28950 Z= 0.343 Chirality : 0.045 0.361 3740 Planarity : 0.005 0.067 3682 Dihedral : 5.750 46.643 3144 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.28 % Favored : 89.62 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.82 (0.16), residues: 3034 helix: 0.63 (0.15), residues: 1226 sheet: -2.68 (0.26), residues: 320 loop : -2.53 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 715 TYR 0.018 0.002 TYR D 167 PHE 0.014 0.001 PHE D 822 TRP 0.023 0.001 TRP C 268 HIS 0.005 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (20922) covalent geometry : angle 0.65210 / 0.34 (28894) SS BOND : bond 0.00464 / 0.31 ( 16) SS BOND : angle 1.78188 / 1.31 ( 32) hydrogen bonds : bond 0.04030 / 2.83 ( 986) hydrogen bonds : angle 4.96066 / 3.52 ( 2790) link_BETA1-4 : bond 0.01025 / 0.52 ( 2) link_BETA1-4 : angle 1.07630 / 0.54 ( 6) link_NAG-ASN : bond 0.00519 / 0.34 ( 6) link_NAG-ASN : angle 4.44680 / 3.24 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 MET cc_start: 0.8629 (mtp) cc_final: 0.8413 (mtp) REVERT: A 636 LEU cc_start: 0.9335 (mt) cc_final: 0.9089 (tp) REVERT: B 161 MET cc_start: 0.8320 (ptp) cc_final: 0.8044 (ptm) REVERT: C 727 MET cc_start: 0.8804 (ptp) cc_final: 0.8257 (ptp) REVERT: C 774 PHE cc_start: 0.8206 (m-80) cc_final: 0.7618 (m-80) REVERT: D 782 GLN cc_start: 0.8697 (tp40) cc_final: 0.8227 (tp40) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.0974 time to fit residues: 31.3513 Evaluate side-chains 157 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: [51, 74, 195, 158, 61, 179, 65, 3, 171, 6, 150] chunk 51 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 195 optimal weight: 0.0770 chunk 158 optimal weight: 5.9990 chunk 61 optimal weight: 0.0770 chunk 179 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 3 optimal weight: 30.0000 chunk 171 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 overall best weight: 3.2302 ------------------------------------------------------------------------------- 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 = 0.3354 r_free = 0.3354 target = 0.063044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.052108 restraints weight = 160386.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.053143 restraints weight = 107728.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.053853 restraints weight = 80579.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.054404 restraints weight = 65313.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.054759 restraints weight = 55792.602| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20946 Z= 0.147 Angle : 0.664 15.138 28950 Z= 0.340 Chirality : 0.046 0.360 3740 Planarity : 0.005 0.065 3682 Dihedral : 5.648 45.492 3144 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.68 % Favored : 89.29 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.72 (0.16), residues: 3034 helix: 0.69 (0.15), residues: 1224 sheet: -2.61 (0.27), residues: 320 loop : -2.47 (0.17), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 743 TYR 0.020 0.002 TYR D 231 PHE 0.029 0.001 PHE B 784 TRP 0.022 0.001 TRP A 268 HIS 0.003 0.001 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (20922) covalent geometry : angle 0.65261 / 0.34 (28894) SS BOND : bond 0.00390 / 0.25 ( 16) SS BOND : angle 1.72260 / 1.33 ( 32) hydrogen bonds : bond 0.03956 / 2.78 ( 986) hydrogen bonds : angle 4.91868 / 3.49 ( 2790) link_BETA1-4 : bond 0.01042 / 0.52 ( 2) link_BETA1-4 : angle 1.11400 / 0.56 ( 6) link_NAG-ASN : bond 0.00534 / 0.34 ( 6) link_NAG-ASN : angle 4.38069 / 3.21 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 728 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7715 (mp0) REVERT: B 161 MET cc_start: 0.8323 (ptp) cc_final: 0.8026 (ptm) REVERT: C 165 LEU cc_start: 0.9429 (tp) cc_final: 0.9161 (tp) REVERT: C 727 MET cc_start: 0.8786 (ptp) cc_final: 0.8338 (ptp) REVERT: C 774 PHE cc_start: 0.8245 (m-80) cc_final: 0.7668 (m-80) REVERT: D 782 GLN cc_start: 0.8779 (tp40) cc_final: 0.8279 (tp40) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.0979 time to fit residues: 31.9296 Evaluate side-chains 159 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: [32, 290, 148, 288, 115, 297, 114, 26, 159, 221, 293] chunk 32 optimal weight: 5.9990 chunk 290 optimal weight: 20.0000 chunk 148 optimal weight: 4.9990 chunk 288 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 297 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 159 optimal weight: 8.9990 chunk 221 optimal weight: 4.9990 chunk 293 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 637 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.062258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.051337 restraints weight = 161207.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.052357 restraints weight = 108117.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.053081 restraints weight = 81055.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.053597 restraints weight = 65606.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.053950 restraints weight = 56199.390| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20946 Z= 0.195 Angle : 0.692 14.249 28950 Z= 0.358 Chirality : 0.046 0.313 3740 Planarity : 0.005 0.063 3682 Dihedral : 5.822 46.421 3144 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.37 % Favored : 88.60 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.82 (0.16), residues: 3034 helix: 0.57 (0.15), residues: 1224 sheet: -2.67 (0.26), residues: 322 loop : -2.48 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 743 TYR 0.022 0.002 TYR D 167 PHE 0.023 0.002 PHE B 784 TRP 0.028 0.002 TRP A 632 HIS 0.005 0.001 HIS C 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (20922) covalent geometry : angle 0.68112 / 0.36 (28894) SS BOND : bond 0.00433 / 0.27 ( 16) SS BOND : angle 1.70667 / 1.31 ( 32) hydrogen bonds : bond 0.04212 / 2.99 ( 986) hydrogen bonds : angle 5.07274 / 3.60 ( 2790) link_BETA1-4 : bond 0.00975 / 0.49 ( 2) link_BETA1-4 : angle 1.14920 / 0.60 ( 6) link_NAG-ASN : bond 0.00521 / 0.33 ( 6) link_NAG-ASN : angle 4.35389 / 3.20 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6068 Ramachandran restraints generated. 3034 Oldfield, 0 Emsley, 3034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 728 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7714 (mp0) REVERT: B 161 MET cc_start: 0.8388 (ptp) cc_final: 0.8081 (ptm) REVERT: C 165 LEU cc_start: 0.9415 (tp) cc_final: 0.9143 (tp) REVERT: C 727 MET cc_start: 0.8837 (ptp) cc_final: 0.8378 (ptp) REVERT: C 774 PHE cc_start: 0.8269 (m-80) cc_final: 0.7717 (m-80) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.0961 time to fit residues: 30.4116 Evaluate side-chains 153 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: [116, 17, 31, 105, 8, 107, 131, 273, 135, 207, 126] chunk 116 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 8 optimal weight: 0.0270 chunk 107 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 273 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 126 optimal weight: 0.4980 overall best weight: 2.5044 ------------------------------------------------------------------------------- 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 = 0.3361 r_free = 0.3361 target = 0.063344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.052411 restraints weight = 159853.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.053440 restraints weight = 107110.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.054191 restraints weight = 80145.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.054683 restraints weight = 64586.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.055071 restraints weight = 55384.975| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20946 Z= 0.132 Angle : 0.648 13.784 28950 Z= 0.331 Chirality : 0.045 0.299 3740 Planarity : 0.005 0.067 3682 Dihedral : 5.552 45.348 3144 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.59 % Favored : 90.38 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.60 (0.16), residues: 3034 helix: 0.79 (0.15), residues: 1224 sheet: -2.58 (0.26), residues: 336 loop : -2.37 (0.17), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 544 TYR 0.024 0.002 TYR B 231 PHE 0.024 0.001 PHE B 182 TRP 0.023 0.001 TRP A 632 HIS 0.003 0.001 HIS D 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (20922) covalent geometry : angle 0.63746 / 0.33 (28894) SS BOND : bond 0.00353 / 0.22 ( 16) SS BOND : angle 1.60074 / 1.21 ( 32) hydrogen bonds : bond 0.03899 / 2.74 ( 986) hydrogen bonds : angle 4.87945 / 3.46 ( 2790) link_BETA1-4 : bond 0.00931 / 0.47 ( 2) link_BETA1-4 : angle 1.01769 / 0.51 ( 6) link_NAG-ASN : bond 0.00573 / 0.36 ( 6) link_NAG-ASN : angle 4.26286 / 3.15 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2847.36 seconds wall clock time: 50 minutes 0.42 seconds (3000.42 seconds total)