Starting phenix.real_space_refine on Thu Mar 5 07:34:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wht_21675/03_2026/6wht_21675.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wht_21675/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6wht_21675/03_2026/6wht_21675.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wht_21675/03_2026/6wht_21675.map" model { file = "/net/cci-nas-00/data/ceres_data/6wht_21675/03_2026/6wht_21675.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wht_21675/03_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 6 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, D, F Time building chain proxies: 7.32, per 1000 atoms: 0.36 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: 1.59 Conformation dependent library (CDL) restraints added in 1.0 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: 0.98 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: 3.48 Time building geometry restraints manager: 2.16 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 - 24.79: 11695 24.79 - 49.59: 443 49.59 - 74.38: 50 74.38 - 99.17: 18 99.17 - 123.96: 6 Dihedral angle restraints: 12212 sinusoidal: 3330 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 12209 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.380 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:1.270 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 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 : 14.471 123.962 6412 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 covalent geometry : bond 0.00635 (20922) covalent geometry : angle 0.85162 (28894) SS BOND : bond 0.00555 ( 16) SS BOND : angle 1.85049 ( 32) hydrogen bonds : bond 0.20521 ( 986) hydrogen bonds : angle 7.82973 ( 2790) link_BETA1-4 : bond 0.06466 ( 2) link_BETA1-4 : angle 9.57062 ( 6) link_NAG-ASN : bond 0.00612 ( 6) link_NAG-ASN : angle 5.16403 ( 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 : 0.599 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: 0.1005 time to fit residues: 35.5755 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 : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: 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... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 147 GLN A 392 HIS B 118 GLN B 159 ASN B 486 HIS B 616 ASN C 50 ASN C 147 GLN C 392 HIS ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.061447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.050654 restraints weight = 162080.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.051661 restraints weight = 107769.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.052342 restraints weight = 80371.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.052868 restraints weight = 65371.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.053181 restraints weight = 55958.254| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20946 Z= 0.187 Angle : 0.755 11.230 28950 Z= 0.398 Chirality : 0.047 0.252 3740 Planarity : 0.005 0.077 3682 Dihedral : 9.811 93.744 3312 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.14 % Favored : 88.66 % Rotamer: Outliers : 0.40 % Allowed : 7.92 % Favored : 91.69 % 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: -3.70 (0.14), residues: 3034 helix: -1.26 (0.13), residues: 1202 sheet: -3.46 (0.24), residues: 308 loop : -3.32 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 715 TYR 0.022 0.002 TYR D 167 PHE 0.018 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 covalent geometry : bond 0.00392 (20922) covalent geometry : angle 0.74239 (28894) SS BOND : bond 0.00506 ( 16) SS BOND : angle 1.78002 ( 32) hydrogen bonds : bond 0.05971 ( 986) hydrogen bonds : angle 6.03611 ( 2790) link_BETA1-4 : bond 0.00894 ( 2) link_BETA1-4 : angle 3.27138 ( 6) link_NAG-ASN : bond 0.00620 ( 6) link_NAG-ASN : angle 4.77225 ( 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 219 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 212 time to evaluate : 0.727 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: 0.8926 (mp) cc_final: 0.8489 (mp) REVERT: A 727 MET cc_start: 0.8631 (ptp) cc_final: 0.8162 (ptt) REVERT: A 774 PHE cc_start: 0.7852 (m-80) cc_final: 0.7209 (m-80) REVERT: C 125 MET cc_start: 0.8789 (mmm) cc_final: 0.8423 (mmm) REVERT: D 89 MET cc_start: 0.7250 (mmm) cc_final: 0.7013 (tpt) REVERT: D 358 MET cc_start: 0.7649 (mmp) cc_final: 0.7393 (mmm) outliers start: 7 outliers final: 2 residues processed: 219 average time/residue: 0.0977 time to fit residues: 38.1982 Evaluate side-chains 164 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 162 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 41 optimal weight: 0.0970 chunk 55 optimal weight: 9.9990 chunk 168 optimal weight: 4.9990 chunk 295 optimal weight: 10.0000 chunk 176 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 279 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 222 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.063078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.052195 restraints weight = 161434.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.053227 restraints weight = 107283.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.053961 restraints weight = 79983.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.054493 restraints weight = 64479.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.054878 restraints weight = 55053.317| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20946 Z= 0.136 Angle : 0.695 11.435 28950 Z= 0.361 Chirality : 0.046 0.283 3740 Planarity : 0.005 0.068 3682 Dihedral : 8.944 86.490 3312 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.18 % Favored : 89.72 % Rotamer: Outliers : 0.17 % Allowed : 5.52 % Favored : 94.31 % 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: -2.84 (0.15), residues: 3034 helix: -0.37 (0.14), residues: 1226 sheet: -3.05 (0.24), residues: 330 loop : -3.01 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 715 TYR 0.029 0.002 TYR A 724 PHE 0.047 0.001 PHE B 241 TRP 0.018 0.001 TRP D 166 HIS 0.005 0.001 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00282 (20922) covalent geometry : angle 0.68171 (28894) SS BOND : bond 0.00589 ( 16) SS BOND : angle 1.49377 ( 32) hydrogen bonds : bond 0.04848 ( 986) hydrogen bonds : angle 5.43819 ( 2790) link_BETA1-4 : bond 0.01291 ( 2) link_BETA1-4 : angle 3.42907 ( 6) link_NAG-ASN : bond 0.00724 ( 6) link_NAG-ASN : angle 4.75961 ( 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: 3 poor density : 200 time to evaluate : 0.766 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: 0.8910 (mp) cc_final: 0.8485 (mp) REVERT: C 165 LEU cc_start: 0.9466 (tp) cc_final: 0.9169 (tp) REVERT: C 671 ASN cc_start: 0.8744 (m-40) cc_final: 0.8084 (t0) REVERT: C 727 MET cc_start: 0.8648 (ptp) cc_final: 0.8369 (ptp) outliers start: 3 outliers final: 1 residues processed: 203 average time/residue: 0.1000 time to fit residues: 36.7240 Evaluate side-chains 164 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 43 optimal weight: 5.9990 chunk 282 optimal weight: 5.9990 chunk 88 optimal weight: 0.2980 chunk 206 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 301 optimal weight: 0.9980 chunk 1 optimal weight: 20.0000 chunk 63 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 242 optimal weight: 6.9990 chunk 276 optimal weight: 20.0000 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS C 134 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 = 0.3361 r_free = 0.3361 target = 0.063202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.052367 restraints weight = 161687.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.053403 restraints weight = 107085.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.054109 restraints weight = 79623.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.054661 restraints weight = 64439.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.055014 restraints weight = 55043.574| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2299 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= 0.143 Angle : 0.677 11.261 28950 Z= 0.350 Chirality : 0.045 0.278 3740 Planarity : 0.005 0.066 3682 Dihedral : 8.581 84.303 3312 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.28 % Favored : 89.55 % Rotamer: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % 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: -2.37 (0.15), residues: 3034 helix: 0.13 (0.15), residues: 1222 sheet: -2.86 (0.24), residues: 342 loop : -2.81 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 544 TYR 0.018 0.002 TYR D 167 PHE 0.039 0.001 PHE B 241 TRP 0.020 0.001 TRP B 166 HIS 0.004 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00302 (20922) covalent geometry : angle 0.66214 (28894) SS BOND : bond 0.00506 ( 16) SS BOND : angle 1.88166 ( 32) hydrogen bonds : bond 0.04355 ( 986) hydrogen bonds : angle 5.21989 ( 2790) link_BETA1-4 : bond 0.01236 ( 2) link_BETA1-4 : angle 3.77278 ( 6) link_NAG-ASN : bond 0.00711 ( 6) link_NAG-ASN : angle 4.75215 ( 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 192 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 655 MET cc_start: 0.8800 (mmp) cc_final: 0.7868 (mmp) REVERT: C 523 MET cc_start: 0.8521 (mmt) cc_final: 0.8008 (tpt) REVERT: C 671 ASN cc_start: 0.8808 (m-40) cc_final: 0.8157 (t0) REVERT: D 89 MET cc_start: 0.7452 (tpt) cc_final: 0.7033 (tpt) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.1032 time to fit residues: 35.5241 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 : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 165 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 chunk 137 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 217 optimal weight: 0.0870 chunk 172 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 156 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 136 optimal weight: 30.0000 chunk 236 optimal weight: 5.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 717 GLN A 801 HIS B 336 ASN C 801 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 = 0.3353 r_free = 0.3353 target = 0.062922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.052022 restraints weight = 160852.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.053058 restraints weight = 107483.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.053798 restraints weight = 80259.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.054181 restraints weight = 64881.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.054644 restraints weight = 57052.182| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20946 Z= 0.162 Angle : 0.677 11.396 28950 Z= 0.351 Chirality : 0.045 0.267 3740 Planarity : 0.005 0.064 3682 Dihedral : 8.439 84.198 3312 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.48 % Favored : 89.42 % Rotamer: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % 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: -2.21 (0.15), residues: 3034 helix: 0.29 (0.15), residues: 1228 sheet: -2.82 (0.24), residues: 342 loop : -2.75 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 715 TYR 0.019 0.002 TYR B 167 PHE 0.041 0.001 PHE B 241 TRP 0.018 0.001 TRP D 166 HIS 0.009 0.002 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00340 (20922) covalent geometry : angle 0.66351 (28894) SS BOND : bond 0.00386 ( 16) SS BOND : angle 1.57172 ( 32) hydrogen bonds : bond 0.04258 ( 986) hydrogen bonds : angle 5.15707 ( 2790) link_BETA1-4 : bond 0.01195 ( 2) link_BETA1-4 : angle 3.71057 ( 6) link_NAG-ASN : bond 0.00688 ( 6) link_NAG-ASN : angle 4.68111 ( 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 185 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 636 LEU cc_start: 0.9389 (mt) cc_final: 0.9042 (tp) REVERT: C 523 MET cc_start: 0.8564 (mmt) cc_final: 0.8344 (mmt) REVERT: C 774 PHE cc_start: 0.8145 (m-80) cc_final: 0.7499 (m-80) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.0987 time to fit residues: 32.4726 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 : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 280 optimal weight: 0.9990 chunk 253 optimal weight: 0.0770 chunk 161 optimal weight: 5.9990 chunk 243 optimal weight: 10.0000 chunk 61 optimal weight: 0.0060 chunk 238 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 102 optimal weight: 0.0770 chunk 134 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 overall best weight: 0.4314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 649 ASN C 717 GLN D 118 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.065117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.054161 restraints weight = 158185.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.055261 restraints weight = 104561.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.056034 restraints weight = 77385.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.056599 restraints weight = 62182.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.056923 restraints weight = 52760.975| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 20946 Z= 0.120 Angle : 0.652 11.913 28950 Z= 0.331 Chirality : 0.045 0.258 3740 Planarity : 0.005 0.067 3682 Dihedral : 7.819 79.292 3312 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.04 % Favored : 91.86 % Rotamer: Outliers : 0.06 % Allowed : 2.28 % Favored : 97.67 % 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: -1.79 (0.15), residues: 3034 helix: 0.64 (0.15), residues: 1228 sheet: -2.42 (0.26), residues: 326 loop : -2.58 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 544 TYR 0.020 0.001 TYR A 724 PHE 0.036 0.001 PHE B 241 TRP 0.023 0.001 TRP B 166 HIS 0.006 0.001 HIS C 592 Details of bonding type rmsd covalent geometry : bond 0.00237 (20922) covalent geometry : angle 0.63590 (28894) SS BOND : bond 0.00660 ( 16) SS BOND : angle 1.94114 ( 32) hydrogen bonds : bond 0.03751 ( 986) hydrogen bonds : angle 4.82284 ( 2790) link_BETA1-4 : bond 0.01142 ( 2) link_BETA1-4 : angle 4.20356 ( 6) link_NAG-ASN : bond 0.00796 ( 6) link_NAG-ASN : angle 4.72004 ( 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 198 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 0.601 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: B 161 MET cc_start: 0.8467 (ptp) cc_final: 0.8265 (ptm) REVERT: C 125 MET cc_start: 0.8702 (mmp) cc_final: 0.8022 (mmm) REVERT: C 522 MET cc_start: 0.9315 (ptp) cc_final: 0.8894 (mpp) REVERT: C 671 ASN cc_start: 0.8691 (m-40) cc_final: 0.8116 (t0) REVERT: D 216 ILE cc_start: 0.8977 (pt) cc_final: 0.8407 (pt) outliers start: 1 outliers final: 0 residues processed: 198 average time/residue: 0.0990 time to fit residues: 34.7456 Evaluate side-chains 163 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 83 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 102 optimal weight: 0.0970 chunk 27 optimal weight: 20.0000 chunk 129 optimal weight: 10.0000 chunk 180 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 277 optimal weight: 5.9990 overall best weight: 5.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS ** B 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 = 0.3337 r_free = 0.3337 target = 0.062343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.051514 restraints weight = 161618.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.052544 restraints weight = 108081.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.053283 restraints weight = 80706.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.053754 restraints weight = 65160.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.054156 restraints weight = 56099.757| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20946 Z= 0.200 Angle : 0.706 11.285 28950 Z= 0.364 Chirality : 0.045 0.243 3740 Planarity : 0.005 0.059 3682 Dihedral : 8.173 84.160 3312 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.88 % Favored : 89.09 % Rotamer: Outliers : 0.06 % Allowed : 1.94 % Favored : 98.01 % 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: -1.89 (0.15), residues: 3034 helix: 0.57 (0.15), residues: 1228 sheet: -2.67 (0.25), residues: 330 loop : -2.59 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 715 TYR 0.024 0.002 TYR B 167 PHE 0.038 0.002 PHE B 241 TRP 0.018 0.002 TRP C 268 HIS 0.006 0.002 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00420 (20922) covalent geometry : angle 0.69264 (28894) SS BOND : bond 0.00685 ( 16) SS BOND : angle 1.89800 ( 32) hydrogen bonds : bond 0.04149 ( 986) hydrogen bonds : angle 5.05114 ( 2790) link_BETA1-4 : bond 0.00963 ( 2) link_BETA1-4 : angle 3.71141 ( 6) link_NAG-ASN : bond 0.00692 ( 6) link_NAG-ASN : angle 4.61424 ( 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 178 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 VAL cc_start: 0.9047 (t) cc_final: 0.8821 (p) REVERT: B 161 MET cc_start: 0.8373 (ptp) cc_final: 0.8163 (ptm) REVERT: B 216 ILE cc_start: 0.9018 (pt) cc_final: 0.8359 (pt) REVERT: B 241 PHE cc_start: 0.8811 (m-80) cc_final: 0.8423 (m-10) REVERT: C 522 MET cc_start: 0.9230 (ptp) cc_final: 0.8860 (mpp) REVERT: C 727 MET cc_start: 0.8647 (ptp) cc_final: 0.8032 (ptm) REVERT: C 774 PHE cc_start: 0.8228 (m-80) cc_final: 0.7711 (m-80) REVERT: D 89 MET cc_start: 0.7573 (tpt) cc_final: 0.7176 (tpt) REVERT: D 98 VAL cc_start: 0.9001 (t) cc_final: 0.8733 (p) REVERT: D 216 ILE cc_start: 0.8553 (pt) cc_final: 0.8344 (pt) outliers start: 1 outliers final: 0 residues processed: 178 average time/residue: 0.0941 time to fit residues: 30.1924 Evaluate side-chains 150 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 208 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 11 optimal weight: 0.0670 chunk 0 optimal weight: 30.0000 chunk 283 optimal weight: 1.9990 chunk 246 optimal weight: 0.0980 chunk 186 optimal weight: 0.0870 chunk 242 optimal weight: 10.0000 chunk 142 optimal weight: 20.0000 chunk 197 optimal weight: 8.9990 chunk 189 optimal weight: 10.0000 overall best weight: 1.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.064214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.053299 restraints weight = 159864.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.054395 restraints weight = 105231.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.055158 restraints weight = 77632.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.055723 restraints weight = 62285.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.056100 restraints weight = 52918.829| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20946 Z= 0.117 Angle : 0.654 11.669 28950 Z= 0.332 Chirality : 0.045 0.324 3740 Planarity : 0.005 0.067 3682 Dihedral : 7.743 79.948 3312 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.37 % Favored : 91.60 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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: 0.81 (0.15), residues: 1226 sheet: -2.29 (0.27), residues: 324 loop : -2.50 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 715 TYR 0.018 0.001 TYR A 724 PHE 0.030 0.001 PHE B 241 TRP 0.022 0.001 TRP D 166 HIS 0.004 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00247 (20922) covalent geometry : angle 0.63930 (28894) SS BOND : bond 0.00399 ( 16) SS BOND : angle 1.60498 ( 32) hydrogen bonds : bond 0.03761 ( 986) hydrogen bonds : angle 4.80632 ( 2790) link_BETA1-4 : bond 0.01102 ( 2) link_BETA1-4 : angle 4.10472 ( 6) link_NAG-ASN : bond 0.00744 ( 6) link_NAG-ASN : angle 4.67343 ( 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 183 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.709 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: B 161 MET cc_start: 0.8312 (ptp) cc_final: 0.7997 (ptm) REVERT: B 216 ILE cc_start: 0.8820 (pt) cc_final: 0.8510 (pt) REVERT: C 125 MET cc_start: 0.8701 (mmp) cc_final: 0.8035 (mmm) REVERT: C 165 LEU cc_start: 0.9414 (tp) cc_final: 0.9160 (tp) REVERT: C 522 MET cc_start: 0.9269 (ptp) cc_final: 0.8812 (mpp) REVERT: C 774 PHE cc_start: 0.8361 (m-80) cc_final: 0.8131 (m-80) REVERT: D 89 MET cc_start: 0.7807 (tpt) cc_final: 0.7268 (tpt) REVERT: D 98 VAL cc_start: 0.8900 (t) cc_final: 0.8653 (p) REVERT: D 354 ASP cc_start: 0.8615 (m-30) cc_final: 0.8382 (m-30) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.0948 time to fit residues: 31.2779 Evaluate side-chains 152 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 51 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 195 optimal weight: 0.2980 chunk 158 optimal weight: 6.9990 chunk 61 optimal weight: 20.0000 chunk 179 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 171 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 chunk 150 optimal weight: 3.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.062609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.051747 restraints weight = 161115.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.052783 restraints weight = 108203.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.053491 restraints weight = 80772.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.054045 restraints weight = 65520.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.054385 restraints weight = 55774.869| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20946 Z= 0.187 Angle : 0.702 11.441 28950 Z= 0.360 Chirality : 0.045 0.311 3740 Planarity : 0.005 0.062 3682 Dihedral : 7.947 82.666 3312 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.81 % Favored : 89.16 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % 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: -1.74 (0.16), residues: 3034 helix: 0.63 (0.15), residues: 1226 sheet: -2.48 (0.27), residues: 318 loop : -2.47 (0.16), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 743 TYR 0.024 0.002 TYR D 167 PHE 0.038 0.002 PHE B 241 TRP 0.022 0.002 TRP C 268 HIS 0.005 0.002 HIS A 498 Details of bonding type rmsd covalent geometry : bond 0.00400 (20922) covalent geometry : angle 0.68965 (28894) SS BOND : bond 0.00450 ( 16) SS BOND : angle 1.55583 ( 32) hydrogen bonds : bond 0.04150 ( 986) hydrogen bonds : angle 5.02425 ( 2790) link_BETA1-4 : bond 0.01142 ( 2) link_BETA1-4 : angle 3.78483 ( 6) link_NAG-ASN : bond 0.00741 ( 6) link_NAG-ASN : angle 4.57538 ( 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 166 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 727 MET cc_start: 0.8581 (ptp) cc_final: 0.8059 (ptm) REVERT: B 98 VAL cc_start: 0.9022 (t) cc_final: 0.8797 (p) REVERT: B 161 MET cc_start: 0.8353 (ptp) cc_final: 0.8048 (ptm) REVERT: B 462 ILE cc_start: 0.9360 (mm) cc_final: 0.9146 (mt) REVERT: C 774 PHE cc_start: 0.8236 (m-80) cc_final: 0.7874 (m-80) REVERT: D 98 VAL cc_start: 0.8980 (t) cc_final: 0.8716 (p) REVERT: D 354 ASP cc_start: 0.8623 (m-30) cc_final: 0.8142 (m-30) REVERT: D 462 ILE cc_start: 0.9372 (mm) cc_final: 0.9162 (mt) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.0975 time to fit residues: 29.4766 Evaluate side-chains 147 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 32 optimal weight: 30.0000 chunk 290 optimal weight: 20.0000 chunk 148 optimal weight: 5.9990 chunk 288 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 297 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 chunk 221 optimal weight: 6.9990 chunk 293 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 637 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.062616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.051757 restraints weight = 160954.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.052779 restraints weight = 107937.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.053479 restraints weight = 80872.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.054013 restraints weight = 65643.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.054360 restraints weight = 56177.060| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20946 Z= 0.184 Angle : 0.700 11.436 28950 Z= 0.359 Chirality : 0.046 0.289 3740 Planarity : 0.005 0.064 3682 Dihedral : 7.976 82.751 3312 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.35 % Favored : 89.62 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % 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: -1.73 (0.16), residues: 3034 helix: 0.62 (0.15), residues: 1226 sheet: -2.57 (0.27), residues: 314 loop : -2.44 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 544 TYR 0.019 0.002 TYR B 167 PHE 0.035 0.002 PHE B 241 TRP 0.025 0.002 TRP C 268 HIS 0.005 0.001 HIS C 498 Details of bonding type rmsd covalent geometry : bond 0.00393 (20922) covalent geometry : angle 0.68590 (28894) SS BOND : bond 0.00461 ( 16) SS BOND : angle 1.86812 ( 32) hydrogen bonds : bond 0.04151 ( 986) hydrogen bonds : angle 5.03372 ( 2790) link_BETA1-4 : bond 0.01102 ( 2) link_BETA1-4 : angle 3.79178 ( 6) link_NAG-ASN : bond 0.00691 ( 6) link_NAG-ASN : angle 4.60647 ( 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 170 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 MET cc_start: 0.8813 (mmt) cc_final: 0.8500 (tpt) REVERT: A 727 MET cc_start: 0.8699 (ptp) cc_final: 0.8132 (ptm) REVERT: A 774 PHE cc_start: 0.8090 (m-80) cc_final: 0.7484 (m-80) REVERT: B 98 VAL cc_start: 0.9048 (t) cc_final: 0.8809 (p) REVERT: B 161 MET cc_start: 0.8359 (ptp) cc_final: 0.8034 (ptm) REVERT: B 462 ILE cc_start: 0.9397 (mm) cc_final: 0.9131 (mt) REVERT: C 165 LEU cc_start: 0.9393 (tp) cc_final: 0.9131 (tp) REVERT: C 723 MET cc_start: 0.8767 (tpp) cc_final: 0.8310 (tpt) REVERT: C 727 MET cc_start: 0.8807 (ptp) cc_final: 0.8587 (ptp) REVERT: C 774 PHE cc_start: 0.8322 (m-80) cc_final: 0.7923 (m-80) REVERT: D 98 VAL cc_start: 0.8957 (t) cc_final: 0.8684 (p) REVERT: D 354 ASP cc_start: 0.8660 (m-30) cc_final: 0.8058 (m-30) REVERT: D 462 ILE cc_start: 0.9404 (mm) cc_final: 0.9131 (mt) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.0949 time to fit residues: 29.3421 Evaluate side-chains 149 residues out of total 2670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 116 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 chunk 8 optimal weight: 0.9980 chunk 107 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 273 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 615 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.064178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.053254 restraints weight = 159450.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.054341 restraints weight = 105306.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.055109 restraints weight = 78102.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.055620 restraints weight = 62645.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.056044 restraints weight = 53454.993| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20946 Z= 0.118 Angle : 0.654 15.045 28950 Z= 0.329 Chirality : 0.045 0.284 3740 Planarity : 0.005 0.066 3682 Dihedral : 7.535 79.140 3312 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.26 % Favored : 90.71 % 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 : 0.10 % 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: -1.46 (0.16), residues: 3034 helix: 0.86 (0.15), residues: 1232 sheet: -2.45 (0.27), residues: 332 loop : -2.30 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 715 TYR 0.021 0.001 TYR B 231 PHE 0.032 0.001 PHE B 241 TRP 0.025 0.001 TRP C 268 HIS 0.003 0.001 HIS A 94 Details of bonding type rmsd covalent geometry : bond 0.00253 (20922) covalent geometry : angle 0.63942 (28894) SS BOND : bond 0.00415 ( 16) SS BOND : angle 1.68792 ( 32) hydrogen bonds : bond 0.03711 ( 986) hydrogen bonds : angle 4.78105 ( 2790) link_BETA1-4 : bond 0.01086 ( 2) link_BETA1-4 : angle 4.13778 ( 6) link_NAG-ASN : bond 0.00849 ( 6) link_NAG-ASN : angle 4.57110 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2820.34 seconds wall clock time: 49 minutes 33.68 seconds (2973.68 seconds total)