Starting phenix.real_space_refine on Sun Sep 13 13:59:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6whw_21678/09_2026/6whw_21678.cif Found real_map, /net/cci-nas-00/data/ceres_data/6whw_21678/09_2026/6whw_21678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6whw_21678/09_2026/6whw_21678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6whw_21678/09_2026/6whw_21678.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6whw_21678/09_2026/6whw_21678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6whw_21678/09_2026/6whw_21678.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6whw_21678/09_2026/6whw_21678.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6whw_21678/09_2026/6whw_21678.cif" } resolution = 4.09 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= -0.019 sd= 0.707 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 142 5.16 5 Cl 4 4.86 5 C 15166 2.51 5 N 3862 2.21 5 O 4464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23640 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 5920 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 32, 'TRANS': 762} Chain breaks: 4 Unresolved non-hydrogen bonds: 372 Unresolved non-hydrogen angles: 439 Unresolved non-hydrogen dihedrals: 321 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 19, 'HIS:plan': 4, 'GLU:plan': 13, 'GLN:plan1': 6, 'ASN:plan1': 4, 'TYR:plan': 2, 'ASP:plan': 7, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 244 Chain: "B" Number of atoms: 5860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5860 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 27, 'TRANS': 757} Chain breaks: 2 Unresolved non-hydrogen bonds: 360 Unresolved non-hydrogen angles: 440 Unresolved non-hydrogen dihedrals: 313 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 4, 'HIS:plan': 3, 'ARG:plan': 12, 'GLU:plan': 17, 'ASP:plan': 6, 'GLN:plan1': 5, 'TYR:plan': 4, 'TRP:plan': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 251 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, D Time building chain proxies: 11.44, per 1000 atoms: 0.48 Number of scatterers: 23640 At special positions: 0 Unit cell: (135.63, 149.33, 184.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 4 17.00 S 142 16.00 P 2 15.00 O 4464 8.00 N 3862 7.00 C 15166 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=2.04 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 A 831 " - pdb=" SG CYS D 557 " distance=2.07 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=2.04 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.04 Simple disulfide: pdb=" SG CYS B 557 " - pdb=" SG CYS C 831 " distance=1.99 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B 902 " - " ASN B 542 " " NAG D 902 " - " ASN D 542 " Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 1.0 seconds 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5900 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 42 sheets defined 42.0% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 35 through 51 removed outlier: 3.590A pdb=" N GLU A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 43 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 74 through 83 removed outlier: 4.141A pdb=" N CYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLU A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 113 removed outlier: 3.571A pdb=" N SER A 108 " --> pdb=" O THR A 105 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N THR A 110 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ALA A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.662A pdb=" N TYR A 128 " --> pdb=" O MET A 125 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER A 129 " --> pdb=" O SER A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 148 removed outlier: 3.846A pdb=" N SER A 148 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 158 removed outlier: 4.205A pdb=" N ARG A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 185 Processing helix chain 'A' and resid 225 through 234 removed outlier: 3.881A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU A 234 " --> pdb=" O MET A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 257 removed outlier: 4.920A pdb=" N VAL A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ALA A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A 257 " --> pdb=" O TYR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 275 Processing helix chain 'A' and resid 276 through 280 Processing helix chain 'A' and resid 297 through 300 Processing helix chain 'A' and resid 301 through 317 removed outlier: 3.653A pdb=" N GLY A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N HIS A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLU A 315 " --> pdb=" O GLN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 347 Processing helix chain 'A' and resid 402 through 406 Processing helix chain 'A' and resid 479 through 492 Processing helix chain 'A' and resid 520 through 528 Processing helix chain 'A' and resid 541 through 546 removed outlier: 3.553A pdb=" N ALA A 545 " --> pdb=" O ASN A 541 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN A 546 " --> pdb=" O ASN A 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 541 through 546' Processing helix chain 'A' and resid 580 through 604 removed outlier: 3.805A pdb=" N TRP A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N HIS A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 601 " --> pdb=" O MET A 597 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG A 603 " --> pdb=" O TYR A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 635 removed outlier: 3.954A pdb=" N LEU A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 679 removed outlier: 3.793A pdb=" N VAL A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 665 " --> pdb=" O ALA A 661 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 695 removed outlier: 3.514A pdb=" N ARG A 694 " --> pdb=" O ASP A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 716 removed outlier: 3.558A pdb=" N ILE A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 728 Processing helix chain 'A' and resid 734 through 743 removed outlier: 3.993A pdb=" N GLN A 740 " --> pdb=" O ALA A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 764 removed outlier: 4.449A pdb=" N PHE A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU A 760 " --> pdb=" O VAL A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 800 removed outlier: 4.034A pdb=" N LEU A 798 " --> pdb=" O SER A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 834 through 859 removed outlier: 3.878A pdb=" N PHE A 838 " --> pdb=" O MET A 834 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 849 " --> pdb=" O ILE A 845 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE A 850 " --> pdb=" O VAL A 846 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N PHE A 853 " --> pdb=" O ILE A 849 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU A 855 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 56 removed outlier: 3.957A pdb=" N ALA B 53 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N HIS B 54 " --> pdb=" O LYS B 51 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS B 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 77 through 93 removed outlier: 4.151A pdb=" N ASP B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU B 88 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N MET B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N SER B 90 " --> pdb=" O CYS B 86 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 118 removed outlier: 3.874A pdb=" N ILE B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 Processing helix chain 'B' and resid 178 through 193 removed outlier: 3.867A pdb=" N PHE B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR B 189 " --> pdb=" O LYS B 185 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 222 removed outlier: 4.020A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS B 222 " --> pdb=" O ASN B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 247 Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 288 through 300 removed outlier: 3.989A pdb=" N ILE B 300 " --> pdb=" O GLY B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 removed outlier: 5.044A pdb=" N LEU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N HIS B 311 " --> pdb=" O MET B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 337 removed outlier: 3.951A pdb=" N SER B 332 " --> pdb=" O ARG B 328 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN B 333 " --> pdb=" O ILE B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 473 Processing helix chain 'B' and resid 498 through 503 Processing helix chain 'B' and resid 516 through 520 Processing helix chain 'B' and resid 548 through 552 removed outlier: 3.551A pdb=" N LEU B 551 " --> pdb=" O SER B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 578 removed outlier: 4.754A pdb=" N PHE B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 615 removed outlier: 3.914A pdb=" N TRP B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 651 removed outlier: 4.360A pdb=" N SER B 633 " --> pdb=" O LYS B 629 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA B 644 " --> pdb=" O VAL B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 689 through 696 removed outlier: 3.768A pdb=" N ARG B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN B 694 " --> pdb=" O SER B 690 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE B 695 " --> pdb=" O THR B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 706 removed outlier: 3.939A pdb=" N MET B 706 " --> pdb=" O MET B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 710 removed outlier: 4.196A pdb=" N ASN B 710 " --> pdb=" O GLY B 707 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 707 through 710' Processing helix chain 'B' and resid 714 through 720 removed outlier: 3.789A pdb=" N SER B 720 " --> pdb=" O ASP B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 741 removed outlier: 3.642A pdb=" N TYR B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 786 removed outlier: 4.672A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.646A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 840 removed outlier: 5.380A pdb=" N GLY B 820 " --> pdb=" O ASP B 816 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL B 821 " --> pdb=" O ASN B 817 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE B 822 " --> pdb=" O MET B 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 51 removed outlier: 3.590A pdb=" N GLU C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN C 40 " --> pdb=" O ARG C 36 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS C 51 " --> pdb=" O ASN C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 73 Processing helix chain 'C' and resid 74 through 83 removed outlier: 4.140A pdb=" N CYS C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLU C 80 " --> pdb=" O LEU C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 113 removed outlier: 3.570A pdb=" N SER C 108 " --> pdb=" O THR C 105 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N THR C 110 " --> pdb=" O VAL C 107 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ALA C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.662A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER C 129 " --> pdb=" O SER C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 148 removed outlier: 3.845A pdb=" N SER C 148 " --> pdb=" O SER C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 158 removed outlier: 4.206A pdb=" N ARG C 156 " --> pdb=" O PHE C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 185 Processing helix chain 'C' and resid 225 through 234 removed outlier: 3.881A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU C 234 " --> pdb=" O MET C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 257 removed outlier: 4.920A pdb=" N VAL C 252 " --> pdb=" O ASP C 248 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ALA C 255 " --> pdb=" O THR C 251 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA C 257 " --> pdb=" O TYR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 275 Processing helix chain 'C' and resid 276 through 280 Processing helix chain 'C' and resid 297 through 300 Processing helix chain 'C' and resid 301 through 317 removed outlier: 3.654A pdb=" N GLY C 307 " --> pdb=" O SER C 303 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL C 308 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL C 309 " --> pdb=" O ALA C 305 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 312 " --> pdb=" O VAL C 308 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N HIS C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLU C 315 " --> pdb=" O GLN C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 347 Processing helix chain 'C' and resid 402 through 406 Processing helix chain 'C' and resid 479 through 492 Processing helix chain 'C' and resid 520 through 528 Processing helix chain 'C' and resid 541 through 546 removed outlier: 3.552A pdb=" N ALA C 545 " --> pdb=" O ASN C 541 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN C 546 " --> pdb=" O ASN C 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 541 through 546' Processing helix chain 'C' and resid 580 through 604 removed outlier: 3.806A pdb=" N TRP C 584 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU C 585 " --> pdb=" O SER C 581 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N HIS C 592 " --> pdb=" O GLY C 588 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU C 601 " --> pdb=" O MET C 597 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG C 603 " --> pdb=" O TYR C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 635 removed outlier: 3.954A pdb=" N LEU C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 679 removed outlier: 3.794A pdb=" N VAL C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL C 665 " --> pdb=" O ALA C 661 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU C 678 " --> pdb=" O ALA C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 695 removed outlier: 3.514A pdb=" N ARG C 694 " --> pdb=" O ASP C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 716 removed outlier: 3.557A pdb=" N ILE C 712 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG C 716 " --> pdb=" O ILE C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 728 Processing helix chain 'C' and resid 734 through 743 removed outlier: 3.994A pdb=" N GLN C 740 " --> pdb=" O ALA C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 764 removed outlier: 4.450A pdb=" N PHE C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU C 760 " --> pdb=" O VAL C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 800 removed outlier: 4.034A pdb=" N LEU C 798 " --> pdb=" O SER C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 814 Processing helix chain 'C' and resid 834 through 859 removed outlier: 3.878A pdb=" N PHE C 838 " --> pdb=" O MET C 834 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE C 849 " --> pdb=" O ILE C 845 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE C 850 " --> pdb=" O VAL C 846 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N PHE C 853 " --> pdb=" O ILE C 849 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE C 854 " --> pdb=" O PHE C 850 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU C 855 " --> pdb=" O LEU C 851 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 856 " --> pdb=" O ILE C 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 56 removed outlier: 3.958A pdb=" N ALA D 53 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS D 54 " --> pdb=" O LYS D 51 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS D 56 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 62 Processing helix chain 'D' and resid 77 through 93 removed outlier: 4.152A pdb=" N ASP D 87 " --> pdb=" O THR D 83 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LEU D 88 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N MET D 89 " --> pdb=" O ILE D 85 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N SER D 90 " --> pdb=" O CYS D 86 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 118 removed outlier: 3.873A pdb=" N ILE D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA D 117 " --> pdb=" O ASP D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 164 Processing helix chain 'D' and resid 178 through 193 removed outlier: 3.867A pdb=" N PHE D 182 " --> pdb=" O GLY D 178 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR D 189 " --> pdb=" O LYS D 185 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU D 191 " --> pdb=" O ARG D 187 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN D 192 " --> pdb=" O SER D 188 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER D 193 " --> pdb=" O THR D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 222 removed outlier: 4.021A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS D 222 " --> pdb=" O ASN D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 247 Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 288 through 300 removed outlier: 3.988A pdb=" N ILE D 300 " --> pdb=" O GLY D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 311 removed outlier: 5.044A pdb=" N LEU D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU D 310 " --> pdb=" O ASP D 306 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS D 311 " --> pdb=" O MET D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 337 removed outlier: 3.952A pdb=" N SER D 332 " --> pdb=" O ARG D 328 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN D 333 " --> pdb=" O ILE D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 473 Processing helix chain 'D' and resid 498 through 503 Processing helix chain 'D' and resid 516 through 520 Processing helix chain 'D' and resid 548 through 552 removed outlier: 3.551A pdb=" N LEU D 551 " --> pdb=" O SER D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 578 removed outlier: 4.754A pdb=" N PHE D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 615 removed outlier: 3.913A pdb=" N TRP D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 651 removed outlier: 4.359A pdb=" N SER D 633 " --> pdb=" O LYS D 629 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA D 644 " --> pdb=" O VAL D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 689 through 696 removed outlier: 3.768A pdb=" N ARG D 693 " --> pdb=" O GLY D 689 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN D 694 " --> pdb=" O SER D 690 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE D 695 " --> pdb=" O THR D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 706 removed outlier: 3.939A pdb=" N MET D 706 " --> pdb=" O MET D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 710 removed outlier: 4.196A pdb=" N ASN D 710 " --> pdb=" O GLY D 707 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 707 through 710' Processing helix chain 'D' and resid 714 through 720 removed outlier: 3.789A pdb=" N SER D 720 " --> pdb=" O ASP D 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.641A pdb=" N TYR D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 786 removed outlier: 4.673A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 797 removed outlier: 3.646A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 840 removed outlier: 5.380A pdb=" N GLY D 820 " --> pdb=" O ASP D 816 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL D 821 " --> pdb=" O ASN D 817 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE D 822 " --> pdb=" O MET D 818 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 60 removed outlier: 7.525A pdb=" N VAL A 87 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ASN A 28 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ALA A 89 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY A 30 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEU A 119 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 215 through 217 removed outlier: 6.388A pdb=" N LEU A 165 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE A 240 " --> pdb=" O LEU A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 289 removed outlier: 3.557A pdb=" N GLN A 378 " --> pdb=" O LYS A 381 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS A 381 " --> pdb=" O GLN A 378 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 360 through 361 removed outlier: 4.443A pdb=" N GLU A 360 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS A 368 " --> pdb=" O GLU A 360 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 371 through 372 Processing sheet with id=AA6, first strand: chain 'A' and resid 497 through 499 removed outlier: 6.316A pdb=" N ILE A 421 " --> pdb=" O HIS A 498 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 535 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N ILE A 534 " --> pdb=" O ARG A 784 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N ARG A 784 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ALA A 536 " --> pdb=" O GLY A 782 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLY A 782 " --> pdb=" O ALA A 536 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU A 538 " --> pdb=" O GLY A 780 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 497 through 499 removed outlier: 6.316A pdb=" N ILE A 421 " --> pdb=" O HIS A 498 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 535 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N ILE A 534 " --> pdb=" O ARG A 784 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N ARG A 784 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ALA A 536 " --> pdb=" O GLY A 782 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLY A 782 " --> pdb=" O ALA A 536 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU A 538 " --> pdb=" O GLY A 780 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN A 557 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LYS A 555 " --> pdb=" O PHE A 779 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 430 through 433 removed outlier: 3.517A pdb=" N TYR A 477 " --> pdb=" O TYR A 431 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 455 " --> pdb=" O CYS A 476 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 509 through 510 Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 703 removed outlier: 7.283A pdb=" N ALA A 703 " --> pdb=" O ILE A 751 " (cutoff:3.500A) removed outlier: 9.745A pdb=" N ASP A 753 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE A 750 " --> pdb=" O LEU A 562 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP A 752 " --> pdb=" O THR A 560 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 37 through 38 removed outlier: 6.754A pdb=" N ILE B 37 " --> pdb=" O GLU B 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 72 through 73 removed outlier: 6.854A pdb=" N LEU B 41 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE B 123 " --> pdb=" O PHE B 144 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 202 through 204 removed outlier: 9.315A pdb=" N LEU B 203 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE B 228 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 278 through 281 removed outlier: 3.525A pdb=" N LEU B 362 " --> pdb=" O TRP B 379 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY B 377 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU B 366 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ARG B 375 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 343 through 344 Processing sheet with id=AB7, first strand: chain 'B' and resid 408 through 410 removed outlier: 6.280A pdb=" N ILE B 408 " --> pdb=" O TYR B 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 417 through 420 Processing sheet with id=AB9, first strand: chain 'B' and resid 508 through 509 Processing sheet with id=AC1, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC2, first strand: chain 'B' and resid 534 through 537 removed outlier: 6.732A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N ASP B 732 " --> pdb=" O GLY B 684 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 655 through 657 removed outlier: 3.928A pdb=" N GLN B 656 " --> pdb=" O VAL B 808 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 59 through 60 removed outlier: 7.525A pdb=" N VAL C 87 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ASN C 28 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ALA C 89 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY C 30 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 215 through 217 removed outlier: 6.388A pdb=" N LEU C 165 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE C 240 " --> pdb=" O LEU C 269 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 288 through 289 removed outlier: 3.557A pdb=" N GLN C 378 " --> pdb=" O LYS C 381 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS C 381 " --> pdb=" O GLN C 378 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 360 through 361 removed outlier: 4.443A pdb=" N GLU C 360 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS C 368 " --> pdb=" O GLU C 360 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 371 through 372 Processing sheet with id=AC9, first strand: chain 'C' and resid 497 through 499 removed outlier: 6.316A pdb=" N ILE C 421 " --> pdb=" O HIS C 498 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL C 535 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N ILE C 534 " --> pdb=" O ARG C 784 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N ARG C 784 " --> pdb=" O ILE C 534 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ALA C 536 " --> pdb=" O GLY C 782 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY C 782 " --> pdb=" O ALA C 536 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU C 538 " --> pdb=" O GLY C 780 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 497 through 499 removed outlier: 6.316A pdb=" N ILE C 421 " --> pdb=" O HIS C 498 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL C 535 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N ILE C 534 " --> pdb=" O ARG C 784 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N ARG C 784 " --> pdb=" O ILE C 534 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ALA C 536 " --> pdb=" O GLY C 782 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLY C 782 " --> pdb=" O ALA C 536 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU C 538 " --> pdb=" O GLY C 780 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN C 557 " --> pdb=" O SER C 777 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LYS C 555 " --> pdb=" O PHE C 779 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 430 through 433 removed outlier: 3.517A pdb=" N TYR C 477 " --> pdb=" O TYR C 431 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 455 " --> pdb=" O CYS C 476 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 509 through 510 Processing sheet with id=AD4, first strand: chain 'C' and resid 702 through 703 removed outlier: 7.283A pdb=" N ALA C 703 " --> pdb=" O ILE C 751 " (cutoff:3.500A) removed outlier: 9.745A pdb=" N ASP C 753 " --> pdb=" O ALA C 703 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE C 750 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP C 752 " --> pdb=" O THR C 560 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 37 through 38 removed outlier: 6.755A pdb=" N ILE D 37 " --> pdb=" O GLU D 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 72 through 73 removed outlier: 6.853A pdb=" N LEU D 41 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE D 123 " --> pdb=" O PHE D 144 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 202 through 204 removed outlier: 9.316A pdb=" N LEU D 203 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE D 228 " --> pdb=" O ILE D 257 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 278 through 281 removed outlier: 3.525A pdb=" N LEU D 362 " --> pdb=" O TRP D 379 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY D 377 " --> pdb=" O ILE D 364 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU D 366 " --> pdb=" O ARG D 375 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ARG D 375 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 343 through 344 Processing sheet with id=AE1, first strand: chain 'D' and resid 408 through 410 removed outlier: 6.280A pdb=" N ILE D 408 " --> pdb=" O TYR D 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'D' and resid 417 through 420 Processing sheet with id=AE3, first strand: chain 'D' and resid 508 through 509 Processing sheet with id=AE4, first strand: chain 'D' and resid 531 through 532 Processing sheet with id=AE5, first strand: chain 'D' and resid 534 through 537 removed outlier: 6.733A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 655 through 657 removed outlier: 3.928A pdb=" N GLN D 656 " --> pdb=" O VAL D 808 " (cutoff:3.500A) 852 hydrogen bonds defined for protein. 2340 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: 6.27 Time building geometry restraints manager: 2.85 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: 7616 1.34 - 1.47: 5948 1.47 - 1.59: 10332 1.59 - 1.71: 6 1.71 - 1.84: 242 Bond restraints: 24144 Sorted by residual: bond pdb=" C1 QGP B 901 " pdb=" P QGP B 901 " ideal model delta sigma weight residual 1.851 1.630 0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C1 QGP D 901 " pdb=" P QGP D 901 " ideal model delta sigma weight residual 1.851 1.631 0.220 2.00e-02 2.50e+03 1.22e+02 bond pdb=" O3 QGP D 901 " pdb=" P QGP D 901 " ideal model delta sigma weight residual 1.629 1.473 0.156 2.00e-02 2.50e+03 6.09e+01 bond pdb=" O3 QGP B 901 " pdb=" P QGP B 901 " ideal model delta sigma weight residual 1.629 1.474 0.155 2.00e-02 2.50e+03 6.00e+01 bond pdb=" C16 QGP B 901 " pdb=" C9 QGP B 901 " ideal model delta sigma weight residual 1.500 1.376 0.124 2.00e-02 2.50e+03 3.84e+01 ... (remaining 24139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 32039 2.29 - 4.57: 775 4.57 - 6.86: 84 6.86 - 9.15: 12 9.15 - 11.43: 2 Bond angle restraints: 32912 Sorted by residual: angle pdb=" C THR B 76 " pdb=" N ASP B 77 " pdb=" CA ASP B 77 " ideal model delta sigma weight residual 123.56 134.99 -11.43 1.98e+00 2.55e-01 3.33e+01 angle pdb=" C THR D 76 " pdb=" N ASP D 77 " pdb=" CA ASP D 77 " ideal model delta sigma weight residual 123.56 134.99 -11.43 1.98e+00 2.55e-01 3.33e+01 angle pdb=" N GLY B 253 " pdb=" CA GLY B 253 " pdb=" C GLY B 253 " ideal model delta sigma weight residual 114.85 108.26 6.59 1.35e+00 5.49e-01 2.38e+01 angle pdb=" N GLY D 253 " pdb=" CA GLY D 253 " pdb=" C GLY D 253 " ideal model delta sigma weight residual 114.85 108.32 6.53 1.35e+00 5.49e-01 2.34e+01 angle pdb=" N VAL C 385 " pdb=" CA VAL C 385 " pdb=" C VAL C 385 " ideal model delta sigma weight residual 113.20 108.62 4.58 9.60e-01 1.09e+00 2.27e+01 ... (remaining 32907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 12720 17.45 - 34.90: 1264 34.90 - 52.36: 196 52.36 - 69.81: 32 69.81 - 87.26: 34 Dihedral angle restraints: 14246 sinusoidal: 5100 harmonic: 9146 Sorted by residual: dihedral pdb=" CB CYS D 86 " pdb=" SG CYS D 86 " pdb=" SG CYS D 321 " pdb=" CB CYS D 321 " ideal model delta sinusoidal sigma weight residual 93.00 10.42 82.58 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS B 86 " pdb=" SG CYS B 86 " pdb=" SG CYS B 321 " pdb=" CB CYS B 321 " ideal model delta sinusoidal sigma weight residual 93.00 10.43 82.57 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS C 765 " pdb=" SG CYS C 765 " pdb=" SG CYS C 819 " pdb=" CB CYS C 819 " ideal model delta sinusoidal sigma weight residual -86.00 -5.87 -80.13 1 1.00e+01 1.00e-02 7.95e+01 ... (remaining 14243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2312 0.039 - 0.078: 1109 0.078 - 0.116: 364 0.116 - 0.155: 63 0.155 - 0.194: 10 Chirality restraints: 3858 Sorted by residual: chirality pdb=" CB VAL B 258 " pdb=" CA VAL B 258 " pdb=" CG1 VAL B 258 " pdb=" CG2 VAL B 258 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.41e-01 chirality pdb=" CB VAL D 258 " pdb=" CA VAL D 258 " pdb=" CG1 VAL D 258 " pdb=" CG2 VAL D 258 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.11e-01 chirality pdb=" CA QGP D 901 " pdb=" N QGP D 901 " pdb=" C QGP D 901 " pdb=" C16 QGP D 901 " both_signs ideal model delta sigma weight residual False 2.42 2.60 -0.18 2.00e-01 2.50e+01 8.08e-01 ... (remaining 3855 not shown) Planarity restraints: 4184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 825 " 0.045 5.00e-02 4.00e+02 6.81e-02 7.43e+00 pdb=" N PRO A 826 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 826 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 826 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 825 " 0.045 5.00e-02 4.00e+02 6.78e-02 7.36e+00 pdb=" N PRO C 826 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO C 826 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 826 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 622 " 0.044 5.00e-02 4.00e+02 6.44e-02 6.64e+00 pdb=" N PRO D 623 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 623 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 623 " 0.037 5.00e-02 4.00e+02 ... (remaining 4181 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 591 2.65 - 3.21: 24560 3.21 - 3.77: 34005 3.77 - 4.34: 44856 4.34 - 4.90: 72564 Nonbonded interactions: 176576 Sorted by model distance: nonbonded pdb=" O ASP D 113 " pdb=" OG SER D 116 " model vdw 2.086 3.040 nonbonded pdb=" O ASP B 113 " pdb=" OG SER B 116 " model vdw 2.086 3.040 nonbonded pdb=" O ASP B 306 " pdb=" OG SER B 309 " model vdw 2.110 3.040 nonbonded pdb=" O ASP D 306 " pdb=" OG SER D 309 " model vdw 2.111 3.040 nonbonded pdb=" O ASN B 694 " pdb=" ND2 ASN B 698 " model vdw 2.174 3.120 ... (remaining 176571 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.010 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 30.110 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 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 : 0.009 0.221 24162 Z= 0.420 Angle : 0.871 11.431 32950 Z= 0.492 Chirality : 0.049 0.194 3858 Planarity : 0.005 0.068 4182 Dihedral : 14.589 87.258 8298 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.80 % Favored : 85.01 % Rotamer: Outliers : 0.74 % Allowed : 11.45 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.22 (0.12), residues: 3128 helix: -3.06 (0.11), residues: 1180 sheet: -3.94 (0.19), residues: 412 loop : -3.67 (0.13), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 822 TYR 0.029 0.002 TYR B 731 PHE 0.037 0.003 PHE C 113 TRP 0.021 0.002 TRP A 632 HIS 0.006 0.001 HIS D 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00904 / 0.42 (24144) covalent geometry : angle 0.86640 / 0.49 (32912) SS BOND : bond 0.01513 / 1.28 ( 16) SS BOND : angle 3.13350 / 2.02 ( 32) hydrogen bonds : bond 0.21845 / 15.22 ( 848) hydrogen bonds : angle 8.69224 / 6.00 ( 2340) link_NAG-ASN : bond 0.00403 / 0.20 ( 2) link_NAG-ASN : angle 0.87187 / 0.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 324 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8099 (tpp) cc_final: 0.7765 (tpp) REVERT: A 125 MET cc_start: 0.8363 (mmt) cc_final: 0.8128 (mmm) REVERT: A 662 MET cc_start: 0.9146 (tmm) cc_final: 0.8901 (tmm) REVERT: A 806 MET cc_start: 0.8062 (mmt) cc_final: 0.7590 (mmt) REVERT: B 73 MET cc_start: 0.7487 (ttm) cc_final: 0.7126 (ttm) REVERT: B 201 GLU cc_start: 0.8061 (mp0) cc_final: 0.7772 (mp0) REVERT: B 307 MET cc_start: 0.6515 (ttp) cc_final: 0.6155 (ttp) REVERT: B 537 MET cc_start: 0.8214 (mmm) cc_final: 0.7865 (ttt) REVERT: B 654 MET cc_start: 0.8929 (mmt) cc_final: 0.8495 (mmm) REVERT: B 677 PHE cc_start: 0.8078 (t80) cc_final: 0.7552 (t80) REVERT: B 681 PHE cc_start: 0.6327 (m-10) cc_final: 0.5990 (m-80) REVERT: B 706 MET cc_start: 0.8954 (mtp) cc_final: 0.8558 (ttm) REVERT: B 824 MET cc_start: 0.5686 (mmt) cc_final: 0.5343 (mmm) REVERT: B 829 MET cc_start: 0.8285 (mtt) cc_final: 0.8051 (mtp) REVERT: C 125 MET cc_start: 0.8292 (mmt) cc_final: 0.7994 (mmm) REVERT: C 330 VAL cc_start: 0.7792 (OUTLIER) cc_final: 0.7386 (m) REVERT: C 662 MET cc_start: 0.9250 (tmm) cc_final: 0.8832 (tmm) REVERT: C 680 ARG cc_start: 0.8138 (mtm110) cc_final: 0.7919 (mmt180) REVERT: D 73 MET cc_start: 0.7419 (ttm) cc_final: 0.7142 (ttm) REVERT: D 134 MET cc_start: 0.8438 (mtp) cc_final: 0.8176 (mtp) REVERT: D 508 MET cc_start: 0.8729 (mtt) cc_final: 0.8478 (mtp) REVERT: D 537 MET cc_start: 0.7918 (mmm) cc_final: 0.7637 (ttt) REVERT: D 631 MET cc_start: 0.8684 (tpp) cc_final: 0.8463 (tpp) REVERT: D 654 MET cc_start: 0.8894 (mmt) cc_final: 0.8520 (mmm) REVERT: D 677 PHE cc_start: 0.8168 (t80) cc_final: 0.7602 (t80) REVERT: D 681 PHE cc_start: 0.6429 (m-10) cc_final: 0.6100 (m-80) REVERT: D 706 MET cc_start: 0.8963 (mtp) cc_final: 0.8565 (ttm) REVERT: D 786 ASP cc_start: 0.8714 (m-30) cc_final: 0.8219 (m-30) REVERT: D 824 MET cc_start: 0.5543 (mmt) cc_final: 0.5343 (mmt) outliers start: 18 outliers final: 8 residues processed: 342 average time/residue: 0.1406 time to fit residues: 78.1576 Evaluate side-chains 268 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 259 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 ASN A 134 HIS A 171 HIS A 291 GLN A 301 HIS A 461 ASN A 763 GLN ** A 801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN B 341 ASN B 357 GLN B 359 HIS B 437 GLN B 703 HIS B 817 ASN C 28 ASN C 134 HIS C 171 HIS C 301 HIS C 461 ASN C 763 GLN C 801 HIS C 824 ASN D 341 ASN D 357 GLN D 359 HIS D 437 GLN D 703 HIS D 817 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.110766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.091695 restraints weight = 58272.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.093351 restraints weight = 42131.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.094507 restraints weight = 33745.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.095332 restraints weight = 28894.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.095870 restraints weight = 25907.540| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24162 Z= 0.133 Angle : 0.630 7.773 32950 Z= 0.340 Chirality : 0.045 0.234 3858 Planarity : 0.005 0.071 4182 Dihedral : 6.340 46.512 3348 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.32 % Favored : 92.55 % Rotamer: Outliers : 0.25 % Allowed : 3.97 % Favored : 95.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.29 (0.14), residues: 3128 helix: -1.11 (0.14), residues: 1198 sheet: -3.39 (0.21), residues: 402 loop : -2.73 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 367 TYR 0.015 0.001 TYR C 253 PHE 0.016 0.002 PHE D 474 TRP 0.014 0.001 TRP D 607 HIS 0.004 0.001 HIS B 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (24144) covalent geometry : angle 0.62536 / 0.34 (32912) SS BOND : bond 0.00517 / 0.36 ( 16) SS BOND : angle 2.41189 / 1.63 ( 32) hydrogen bonds : bond 0.04657 / 3.25 ( 848) hydrogen bonds : angle 5.65223 / 3.89 ( 2340) link_NAG-ASN : bond 0.00122 / 0.06 ( 2) link_NAG-ASN : angle 0.57821 / 0.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 351 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8165 (mmt) cc_final: 0.7945 (mmm) REVERT: A 149 SER cc_start: 0.7778 (m) cc_final: 0.7546 (t) REVERT: A 163 ILE cc_start: 0.8952 (pt) cc_final: 0.8750 (pt) REVERT: A 375 MET cc_start: 0.8078 (tpp) cc_final: 0.7769 (tpp) REVERT: B 94 ILE cc_start: 0.6786 (mm) cc_final: 0.6374 (mm) REVERT: B 127 HIS cc_start: 0.7081 (t70) cc_final: 0.6876 (t-170) REVERT: B 307 MET cc_start: 0.6812 (ttp) cc_final: 0.6100 (tmm) REVERT: B 473 LYS cc_start: 0.8947 (mtmm) cc_final: 0.8669 (mttp) REVERT: B 677 PHE cc_start: 0.8001 (t80) cc_final: 0.7518 (t80) REVERT: B 824 MET cc_start: 0.6162 (mmt) cc_final: 0.5907 (mmt) REVERT: C 149 SER cc_start: 0.7875 (m) cc_final: 0.7515 (t) REVERT: C 336 TRP cc_start: 0.7364 (t60) cc_final: 0.7110 (t60) REVERT: C 375 MET cc_start: 0.8023 (tpp) cc_final: 0.7757 (tpp) REVERT: C 686 THR cc_start: 0.8680 (p) cc_final: 0.8369 (t) REVERT: C 723 MET cc_start: 0.8591 (mtp) cc_final: 0.8222 (mtm) REVERT: D 307 MET cc_start: 0.6378 (ttp) cc_final: 0.6029 (tmm) REVERT: D 473 LYS cc_start: 0.8936 (mtmm) cc_final: 0.8667 (mttp) REVERT: D 677 PHE cc_start: 0.8006 (t80) cc_final: 0.7558 (t80) REVERT: D 824 MET cc_start: 0.5428 (mmt) cc_final: 0.4996 (mmm) outliers start: 6 outliers final: 2 residues processed: 357 average time/residue: 0.1367 time to fit residues: 80.0937 Evaluate side-chains 261 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 259 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 155 optimal weight: 4.9990 chunk 279 optimal weight: 3.9990 chunk 119 optimal weight: 50.0000 chunk 295 optimal weight: 0.1980 chunk 145 optimal weight: 9.9990 chunk 289 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 197 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 HIS B 491 ASN C 291 GLN C 801 HIS D 491 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.110285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.091021 restraints weight = 58596.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.092676 restraints weight = 42848.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.093837 restraints weight = 34213.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.094653 restraints weight = 29337.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.095098 restraints weight = 26350.141| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 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 : 0.004 0.060 24162 Z= 0.156 Angle : 0.612 7.540 32950 Z= 0.328 Chirality : 0.045 0.254 3858 Planarity : 0.005 0.135 4182 Dihedral : 6.088 48.814 3348 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.21 % Favored : 90.70 % Rotamer: Outliers : 0.08 % Allowed : 4.26 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.14), residues: 3128 helix: -0.55 (0.15), residues: 1218 sheet: -3.29 (0.21), residues: 436 loop : -2.42 (0.15), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 716 TYR 0.019 0.001 TYR C 253 PHE 0.019 0.002 PHE D 784 TRP 0.014 0.001 TRP D 607 HIS 0.007 0.001 HIS C 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (24144) covalent geometry : angle 0.60821 / 0.33 (32912) SS BOND : bond 0.00474 / 0.30 ( 16) SS BOND : angle 2.38875 / 1.62 ( 32) hydrogen bonds : bond 0.04441 / 3.13 ( 848) hydrogen bonds : angle 5.36371 / 3.67 ( 2340) link_NAG-ASN : bond 0.00012 / 0.01 ( 2) link_NAG-ASN : angle 0.65680 / 0.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 324 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8153 (mmt) cc_final: 0.7938 (mmm) REVERT: A 149 SER cc_start: 0.7894 (m) cc_final: 0.7551 (t) REVERT: A 336 TRP cc_start: 0.7282 (t60) cc_final: 0.6923 (t60) REVERT: A 375 MET cc_start: 0.8102 (tpp) cc_final: 0.7804 (tpp) REVERT: B 307 MET cc_start: 0.6821 (ttp) cc_final: 0.6161 (tmm) REVERT: B 824 MET cc_start: 0.6183 (mmt) cc_final: 0.5939 (mmt) REVERT: C 149 SER cc_start: 0.8030 (m) cc_final: 0.7741 (t) REVERT: C 686 THR cc_start: 0.8635 (p) cc_final: 0.8310 (t) REVERT: C 723 MET cc_start: 0.8538 (mtp) cc_final: 0.8209 (mtm) REVERT: D 73 MET cc_start: 0.7611 (ttm) cc_final: 0.7406 (ttm) outliers start: 2 outliers final: 0 residues processed: 326 average time/residue: 0.1339 time to fit residues: 72.6939 Evaluate side-chains 258 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 224 optimal weight: 0.9990 chunk 196 optimal weight: 0.2980 chunk 216 optimal weight: 6.9990 chunk 168 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 306 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 801 HIS C 520 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.112038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.092869 restraints weight = 58287.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.094537 restraints weight = 42201.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.095721 restraints weight = 33682.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.096520 restraints weight = 28810.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.097097 restraints weight = 25867.830| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24162 Z= 0.130 Angle : 0.581 8.107 32950 Z= 0.310 Chirality : 0.044 0.238 3858 Planarity : 0.005 0.114 4182 Dihedral : 5.713 48.738 3348 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.32 % Favored : 92.58 % Rotamer: Outliers : 0.12 % Allowed : 3.22 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.15), residues: 3128 helix: -0.12 (0.15), residues: 1218 sheet: -2.92 (0.23), residues: 436 loop : -2.17 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 716 TYR 0.010 0.001 TYR D 282 PHE 0.017 0.002 PHE C 774 TRP 0.019 0.001 TRP C 632 HIS 0.007 0.001 HIS A 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (24144) covalent geometry : angle 0.57697 / 0.31 (32912) SS BOND : bond 0.00484 / 0.33 ( 16) SS BOND : angle 2.20083 / 1.51 ( 32) hydrogen bonds : bond 0.03984 / 2.81 ( 848) hydrogen bonds : angle 5.04831 / 3.45 ( 2340) link_NAG-ASN : bond 0.00031 / 0.02 ( 2) link_NAG-ASN : angle 0.62447 / 0.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 344 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8009 (mmt) cc_final: 0.7798 (mmt) REVERT: A 149 SER cc_start: 0.7835 (m) cc_final: 0.7524 (t) REVERT: A 375 MET cc_start: 0.7832 (tpp) cc_final: 0.7534 (tpp) REVERT: A 585 LEU cc_start: 0.8801 (mm) cc_final: 0.8582 (mm) REVERT: A 774 PHE cc_start: 0.7384 (t80) cc_final: 0.7176 (t80) REVERT: B 307 MET cc_start: 0.6771 (ttp) cc_final: 0.6107 (tmm) REVERT: B 777 ASP cc_start: 0.8303 (m-30) cc_final: 0.8067 (m-30) REVERT: B 824 MET cc_start: 0.6118 (mmt) cc_final: 0.5790 (mmp) REVERT: C 149 SER cc_start: 0.7989 (m) cc_final: 0.7702 (t) REVERT: C 336 TRP cc_start: 0.7387 (t60) cc_final: 0.7166 (t60) REVERT: C 686 THR cc_start: 0.8721 (p) cc_final: 0.8391 (t) REVERT: C 716 ARG cc_start: 0.7795 (ptm160) cc_final: 0.7473 (ptm160) REVERT: C 723 MET cc_start: 0.8503 (mtp) cc_final: 0.8210 (mtm) REVERT: D 777 ASP cc_start: 0.8219 (m-30) cc_final: 0.7974 (m-30) REVERT: D 786 ASP cc_start: 0.8005 (m-30) cc_final: 0.7623 (m-30) REVERT: D 824 MET cc_start: 0.5728 (mmt) cc_final: 0.5370 (mmm) REVERT: D 837 ILE cc_start: 0.7513 (mm) cc_final: 0.7253 (mt) outliers start: 3 outliers final: 0 residues processed: 346 average time/residue: 0.1323 time to fit residues: 76.0729 Evaluate side-chains 261 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 311 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 224 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 260 optimal weight: 8.9990 chunk 305 optimal weight: 8.9990 chunk 173 optimal weight: 4.9990 chunk 280 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 HIS ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.113255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.094012 restraints weight = 58041.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.095680 restraints weight = 41983.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.096864 restraints weight = 33652.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.097679 restraints weight = 28811.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.098146 restraints weight = 25869.920| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24162 Z= 0.112 Angle : 0.563 9.257 32950 Z= 0.299 Chirality : 0.044 0.334 3858 Planarity : 0.004 0.102 4182 Dihedral : 5.396 47.529 3348 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.77 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.15), residues: 3128 helix: 0.06 (0.15), residues: 1228 sheet: -2.63 (0.24), residues: 430 loop : -2.00 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 716 TYR 0.014 0.001 TYR C 668 PHE 0.016 0.001 PHE B 842 TRP 0.013 0.001 TRP D 607 HIS 0.006 0.001 HIS C 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (24144) covalent geometry : angle 0.55991 / 0.30 (32912) SS BOND : bond 0.00434 / 0.28 ( 16) SS BOND : angle 2.07172 / 1.42 ( 32) hydrogen bonds : bond 0.03694 / 2.59 ( 848) hydrogen bonds : angle 4.82216 / 3.30 ( 2340) link_NAG-ASN : bond 0.00055 / 0.03 ( 2) link_NAG-ASN : angle 0.63653 / 0.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 0.734 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 149 SER cc_start: 0.7799 (m) cc_final: 0.7457 (t) REVERT: A 375 MET cc_start: 0.7696 (tpp) cc_final: 0.7363 (tpp) REVERT: A 585 LEU cc_start: 0.8781 (mm) cc_final: 0.8531 (mm) REVERT: B 307 MET cc_start: 0.6697 (ttp) cc_final: 0.6075 (tmm) REVERT: B 615 ASN cc_start: 0.7184 (m-40) cc_final: 0.6456 (p0) REVERT: B 677 PHE cc_start: 0.7952 (t80) cc_final: 0.7621 (t80) REVERT: B 706 MET cc_start: 0.8596 (ttm) cc_final: 0.8357 (ttm) REVERT: B 824 MET cc_start: 0.6073 (mmt) cc_final: 0.5687 (mmp) REVERT: C 149 SER cc_start: 0.7972 (m) cc_final: 0.7679 (t) REVERT: C 491 MET cc_start: 0.7239 (mtt) cc_final: 0.7016 (mtt) REVERT: C 686 THR cc_start: 0.8713 (p) cc_final: 0.8386 (t) REVERT: C 723 MET cc_start: 0.8406 (mtp) cc_final: 0.8069 (mtm) REVERT: D 470 LYS cc_start: 0.8714 (mmmt) cc_final: 0.8492 (tppt) REVERT: D 777 ASP cc_start: 0.8188 (m-30) cc_final: 0.7941 (m-30) REVERT: D 824 MET cc_start: 0.5632 (mmt) cc_final: 0.5270 (mmm) REVERT: D 837 ILE cc_start: 0.7541 (mm) cc_final: 0.7283 (mt) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.1281 time to fit residues: 74.3337 Evaluate side-chains 262 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 119 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 10 optimal weight: 0.0050 chunk 274 optimal weight: 0.6980 chunk 123 optimal weight: 0.0670 chunk 56 optimal weight: 5.9990 chunk 261 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 250 optimal weight: 1.9990 chunk 312 optimal weight: 1.9990 overall best weight: 0.5134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.115940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.096783 restraints weight = 57858.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.098539 restraints weight = 41464.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.099751 restraints weight = 32928.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.100509 restraints weight = 28109.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.101178 restraints weight = 25252.236| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 24162 Z= 0.098 Angle : 0.550 9.916 32950 Z= 0.290 Chirality : 0.043 0.338 3858 Planarity : 0.004 0.105 4182 Dihedral : 4.983 44.586 3348 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.49 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.15), residues: 3128 helix: 0.31 (0.15), residues: 1228 sheet: -2.29 (0.24), residues: 452 loop : -1.83 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 776 TYR 0.011 0.001 TYR D 282 PHE 0.022 0.001 PHE B 681 TRP 0.017 0.001 TRP C 632 HIS 0.008 0.001 HIS B 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (24144) covalent geometry : angle 0.54636 / 0.29 (32912) SS BOND : bond 0.00337 / 0.20 ( 16) SS BOND : angle 2.21117 / 1.56 ( 32) hydrogen bonds : bond 0.03219 / 2.25 ( 848) hydrogen bonds : angle 4.55081 / 3.11 ( 2340) link_NAG-ASN : bond 0.00088 / 0.04 ( 2) link_NAG-ASN : angle 0.65458 / 0.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 SER cc_start: 0.7779 (m) cc_final: 0.7450 (t) REVERT: A 375 MET cc_start: 0.7608 (tpp) cc_final: 0.6892 (tpp) REVERT: A 585 LEU cc_start: 0.8749 (mm) cc_final: 0.8548 (mm) REVERT: B 94 ILE cc_start: 0.6928 (mm) cc_final: 0.6489 (mm) REVERT: B 307 MET cc_start: 0.6507 (ttp) cc_final: 0.6036 (tmm) REVERT: B 615 ASN cc_start: 0.6832 (m-40) cc_final: 0.6360 (p0) REVERT: B 641 ILE cc_start: 0.9506 (tp) cc_final: 0.9275 (tp) REVERT: B 824 MET cc_start: 0.6093 (mmt) cc_final: 0.5709 (mmp) REVERT: C 149 SER cc_start: 0.7892 (m) cc_final: 0.7617 (t) REVERT: C 491 MET cc_start: 0.7152 (mtt) cc_final: 0.6537 (mtt) REVERT: C 493 PHE cc_start: 0.8027 (m-10) cc_final: 0.7822 (m-10) REVERT: C 585 LEU cc_start: 0.8674 (mm) cc_final: 0.8438 (mm) REVERT: C 686 THR cc_start: 0.8652 (p) cc_final: 0.8348 (t) REVERT: C 723 MET cc_start: 0.8516 (mtp) cc_final: 0.8082 (mtm) REVERT: D 157 MET cc_start: 0.7886 (mtt) cc_final: 0.7662 (mtt) REVERT: D 307 MET cc_start: 0.6319 (ttp) cc_final: 0.5810 (tmm) REVERT: D 498 ILE cc_start: 0.8761 (mm) cc_final: 0.8535 (mm) REVERT: D 615 ASN cc_start: 0.6581 (m-40) cc_final: 0.6171 (p0) REVERT: D 641 ILE cc_start: 0.9538 (tp) cc_final: 0.9266 (tp) REVERT: D 706 MET cc_start: 0.8574 (ttm) cc_final: 0.8351 (ttm) REVERT: D 837 ILE cc_start: 0.7530 (mm) cc_final: 0.7254 (mt) outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 0.1301 time to fit residues: 77.9542 Evaluate side-chains 268 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 298 optimal weight: 0.0570 chunk 203 optimal weight: 0.3980 chunk 178 optimal weight: 0.0770 chunk 53 optimal weight: 8.9990 chunk 148 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 219 optimal weight: 0.6980 chunk 230 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 520 ASN A 592 HIS B 127 HIS ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 592 HIS C 726 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.117135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.097683 restraints weight = 57636.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.099447 restraints weight = 41242.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.100676 restraints weight = 32599.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.101571 restraints weight = 27808.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.102180 restraints weight = 24811.131| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 24162 Z= 0.093 Angle : 0.535 8.863 32950 Z= 0.281 Chirality : 0.043 0.337 3858 Planarity : 0.004 0.092 4182 Dihedral : 4.724 41.863 3348 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.15), residues: 3128 helix: 0.50 (0.16), residues: 1206 sheet: -2.02 (0.23), residues: 490 loop : -1.73 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 716 TYR 0.010 0.001 TYR D 282 PHE 0.016 0.001 PHE A 113 TRP 0.012 0.001 TRP D 607 HIS 0.005 0.000 HIS D 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 (24144) covalent geometry : angle 0.53237 / 0.28 (32912) SS BOND : bond 0.00298 / 0.17 ( 16) SS BOND : angle 1.76946 / 1.26 ( 32) hydrogen bonds : bond 0.03017 / 2.10 ( 848) hydrogen bonds : angle 4.43552 / 3.04 ( 2340) link_NAG-ASN : bond 0.00125 / 0.06 ( 2) link_NAG-ASN : angle 0.65707 / 0.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ILE cc_start: 0.8881 (pt) cc_final: 0.8572 (pt) REVERT: A 375 MET cc_start: 0.7431 (tpp) cc_final: 0.6818 (tpp) REVERT: B 94 ILE cc_start: 0.6902 (mm) cc_final: 0.6500 (mm) REVERT: B 307 MET cc_start: 0.6389 (ttp) cc_final: 0.5968 (tmm) REVERT: B 537 MET cc_start: 0.8306 (tpp) cc_final: 0.8017 (ttm) REVERT: B 615 ASN cc_start: 0.6567 (m-40) cc_final: 0.6187 (p0) REVERT: B 824 MET cc_start: 0.6071 (mmt) cc_final: 0.5615 (mmp) REVERT: C 149 SER cc_start: 0.7816 (m) cc_final: 0.7576 (t) REVERT: C 375 MET cc_start: 0.7513 (tpp) cc_final: 0.6893 (tpp) REVERT: C 491 MET cc_start: 0.7033 (mtt) cc_final: 0.6764 (mtt) REVERT: C 628 MET cc_start: 0.7892 (mmm) cc_final: 0.7669 (mmm) REVERT: C 686 THR cc_start: 0.8689 (p) cc_final: 0.8399 (t) REVERT: C 723 MET cc_start: 0.8342 (mtp) cc_final: 0.8031 (mtm) REVERT: D 157 MET cc_start: 0.7844 (mtt) cc_final: 0.7617 (mtt) REVERT: D 307 MET cc_start: 0.6223 (ttp) cc_final: 0.5711 (tmm) REVERT: D 537 MET cc_start: 0.7771 (ttp) cc_final: 0.7465 (ttp) REVERT: D 615 ASN cc_start: 0.6459 (m-40) cc_final: 0.6101 (p0) REVERT: D 671 PHE cc_start: 0.5847 (t80) cc_final: 0.5644 (t80) REVERT: D 837 ILE cc_start: 0.7535 (mm) cc_final: 0.7259 (mt) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.1264 time to fit residues: 76.3615 Evaluate side-chains 273 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 308 optimal weight: 0.9980 chunk 181 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 195 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 105 optimal weight: 0.8980 chunk 244 optimal weight: 0.9980 chunk 153 optimal weight: 5.9990 chunk 267 optimal weight: 6.9990 chunk 298 optimal weight: 1.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 127 HIS ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.113229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.093672 restraints weight = 58038.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.095359 restraints weight = 41758.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.096532 restraints weight = 33344.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.097369 restraints weight = 28542.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.097852 restraints weight = 25588.193| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24162 Z= 0.153 Angle : 0.594 8.480 32950 Z= 0.312 Chirality : 0.045 0.339 3858 Planarity : 0.004 0.091 4182 Dihedral : 5.032 42.048 3348 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.15), residues: 3128 helix: 0.39 (0.15), residues: 1212 sheet: -1.99 (0.25), residues: 452 loop : -1.70 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 716 TYR 0.009 0.001 TYR B 231 PHE 0.028 0.002 PHE A 137 TRP 0.013 0.001 TRP D 607 HIS 0.006 0.001 HIS B 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (24144) covalent geometry : angle 0.59080 / 0.31 (32912) SS BOND : bond 0.00638 / 0.50 ( 16) SS BOND : angle 2.08986 / 1.51 ( 32) hydrogen bonds : bond 0.03846 / 2.72 ( 848) hydrogen bonds : angle 4.63414 / 3.18 ( 2340) link_NAG-ASN : bond 0.00040 / 0.02 ( 2) link_NAG-ASN : angle 0.66090 / 0.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 LEU cc_start: 0.4573 (tp) cc_final: 0.4218 (pt) REVERT: A 375 MET cc_start: 0.7463 (tpp) cc_final: 0.6791 (tpp) REVERT: A 768 VAL cc_start: 0.9346 (p) cc_final: 0.9099 (t) REVERT: B 300 ILE cc_start: 0.8028 (tt) cc_final: 0.7815 (tt) REVERT: B 544 THR cc_start: 0.7820 (t) cc_final: 0.7586 (t) REVERT: B 615 ASN cc_start: 0.6532 (m-40) cc_final: 0.5765 (p0) REVERT: B 641 ILE cc_start: 0.9583 (tp) cc_final: 0.9351 (tp) REVERT: B 824 MET cc_start: 0.6167 (mmt) cc_final: 0.5803 (mmp) REVERT: B 837 ILE cc_start: 0.7142 (mm) cc_final: 0.6807 (mt) REVERT: C 149 SER cc_start: 0.7899 (m) cc_final: 0.7614 (t) REVERT: C 375 MET cc_start: 0.7356 (tpp) cc_final: 0.6646 (tpp) REVERT: C 628 MET cc_start: 0.8113 (mmm) cc_final: 0.7899 (mmm) REVERT: C 686 THR cc_start: 0.8750 (p) cc_final: 0.8438 (t) REVERT: C 723 MET cc_start: 0.8622 (mtp) cc_final: 0.8292 (mtm) REVERT: C 768 VAL cc_start: 0.9349 (p) cc_final: 0.9103 (t) REVERT: D 615 ASN cc_start: 0.6621 (m-40) cc_final: 0.6087 (p0) REVERT: D 837 ILE cc_start: 0.7579 (mm) cc_final: 0.7305 (mt) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.1204 time to fit residues: 68.9731 Evaluate side-chains 265 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 42 optimal weight: 3.9990 chunk 224 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 240 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 155 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 GLN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 802 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.115655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.096191 restraints weight = 57773.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.097897 restraints weight = 41786.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.099099 restraints weight = 33446.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.099970 restraints weight = 28609.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.100535 restraints weight = 25559.839| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 24162 Z= 0.101 Angle : 0.548 7.517 32950 Z= 0.287 Chirality : 0.043 0.320 3858 Planarity : 0.004 0.081 4182 Dihedral : 4.745 39.605 3348 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.15), residues: 3128 helix: 0.67 (0.16), residues: 1188 sheet: -1.67 (0.26), residues: 424 loop : -1.58 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 716 TYR 0.010 0.001 TYR B 231 PHE 0.020 0.001 PHE A 774 TRP 0.018 0.001 TRP C 632 HIS 0.004 0.001 HIS B 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (24144) covalent geometry : angle 0.54577 / 0.29 (32912) SS BOND : bond 0.00360 / 0.24 ( 16) SS BOND : angle 1.79078 / 1.30 ( 32) hydrogen bonds : bond 0.03210 / 2.25 ( 848) hydrogen bonds : angle 4.46424 / 3.06 ( 2340) link_NAG-ASN : bond 0.00106 / 0.05 ( 2) link_NAG-ASN : angle 0.63653 / 0.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 MET cc_start: 0.7455 (tpp) cc_final: 0.6839 (tpp) REVERT: A 628 MET cc_start: 0.7991 (mmm) cc_final: 0.7790 (mmm) REVERT: A 768 VAL cc_start: 0.9328 (p) cc_final: 0.9080 (t) REVERT: B 300 ILE cc_start: 0.7913 (tt) cc_final: 0.7698 (tt) REVERT: B 307 MET cc_start: 0.6613 (ttp) cc_final: 0.5909 (tmm) REVERT: B 615 ASN cc_start: 0.6354 (m-40) cc_final: 0.5699 (p0) REVERT: B 641 ILE cc_start: 0.9570 (tp) cc_final: 0.9289 (tp) REVERT: B 824 MET cc_start: 0.6099 (mmt) cc_final: 0.5669 (mmp) REVERT: B 837 ILE cc_start: 0.7048 (mm) cc_final: 0.6754 (mt) REVERT: C 149 SER cc_start: 0.7938 (m) cc_final: 0.7637 (t) REVERT: C 155 MET cc_start: 0.8152 (mtt) cc_final: 0.7819 (mmm) REVERT: C 235 LEU cc_start: 0.8526 (mp) cc_final: 0.8311 (mp) REVERT: C 375 MET cc_start: 0.7306 (tpp) cc_final: 0.6627 (tpp) REVERT: C 585 LEU cc_start: 0.8658 (mm) cc_final: 0.8434 (mm) REVERT: C 686 THR cc_start: 0.8682 (p) cc_final: 0.8371 (t) REVERT: C 723 MET cc_start: 0.8437 (mtp) cc_final: 0.8119 (mtm) REVERT: C 768 VAL cc_start: 0.9332 (p) cc_final: 0.9078 (t) REVERT: D 615 ASN cc_start: 0.6478 (m-40) cc_final: 0.6031 (p0) REVERT: D 641 ILE cc_start: 0.9551 (tp) cc_final: 0.9334 (tp) REVERT: D 837 ILE cc_start: 0.7562 (mm) cc_final: 0.7279 (mt) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.1172 time to fit residues: 65.9900 Evaluate side-chains 276 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 177 optimal weight: 0.8980 chunk 293 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 188 optimal weight: 7.9990 chunk 219 optimal weight: 0.0570 chunk 26 optimal weight: 10.0000 chunk 307 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 GLN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 HIS ** 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 = 0.3548 r_free = 0.3548 target = 0.114097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.094526 restraints weight = 57916.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.096192 restraints weight = 41751.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.097395 restraints weight = 33423.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.098249 restraints weight = 28624.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.098832 restraints weight = 25610.502| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24162 Z= 0.130 Angle : 0.567 8.272 32950 Z= 0.296 Chirality : 0.044 0.322 3858 Planarity : 0.004 0.075 4182 Dihedral : 4.827 38.122 3348 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.15), residues: 3128 helix: 0.59 (0.16), residues: 1202 sheet: -1.90 (0.25), residues: 458 loop : -1.58 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 712 TYR 0.010 0.001 TYR A 495 PHE 0.022 0.002 PHE D 671 TRP 0.017 0.001 TRP C 632 HIS 0.005 0.001 HIS B 840 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (24144) covalent geometry : angle 0.56396 / 0.29 (32912) SS BOND : bond 0.00443 / 0.30 ( 16) SS BOND : angle 1.83962 / 1.35 ( 32) hydrogen bonds : bond 0.03556 / 2.51 ( 848) hydrogen bonds : angle 4.56301 / 3.12 ( 2340) link_NAG-ASN : bond 0.00066 / 0.03 ( 2) link_NAG-ASN : angle 0.64481 / 0.29 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.8211 (mtt) cc_final: 0.7973 (mmm) REVERT: A 235 LEU cc_start: 0.8690 (mp) cc_final: 0.8476 (mp) REVERT: A 375 MET cc_start: 0.7501 (tpp) cc_final: 0.6856 (tpp) REVERT: A 628 MET cc_start: 0.8134 (mmm) cc_final: 0.7904 (mmm) REVERT: A 768 VAL cc_start: 0.9359 (p) cc_final: 0.9097 (t) REVERT: B 307 MET cc_start: 0.6710 (ttp) cc_final: 0.5989 (tmm) REVERT: B 615 ASN cc_start: 0.6609 (m-40) cc_final: 0.5753 (p0) REVERT: B 641 ILE cc_start: 0.9574 (tp) cc_final: 0.9351 (tp) REVERT: B 824 MET cc_start: 0.6234 (mmt) cc_final: 0.5835 (mmp) REVERT: B 837 ILE cc_start: 0.7164 (mm) cc_final: 0.6858 (mt) REVERT: C 149 SER cc_start: 0.8010 (m) cc_final: 0.7741 (t) REVERT: C 155 MET cc_start: 0.8110 (mtt) cc_final: 0.7866 (mmm) REVERT: C 375 MET cc_start: 0.7200 (tpp) cc_final: 0.6579 (tpp) REVERT: C 686 THR cc_start: 0.8736 (p) cc_final: 0.8427 (t) REVERT: C 716 ARG cc_start: 0.7751 (ptm160) cc_final: 0.7490 (ttt180) REVERT: C 723 MET cc_start: 0.8557 (mtp) cc_final: 0.8242 (mtm) REVERT: C 768 VAL cc_start: 0.9351 (p) cc_final: 0.9102 (t) REVERT: D 615 ASN cc_start: 0.6664 (m-40) cc_final: 0.6084 (p0) REVERT: D 641 ILE cc_start: 0.9529 (tp) cc_final: 0.9295 (tp) REVERT: D 837 ILE cc_start: 0.7584 (mm) cc_final: 0.7299 (mt) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.1237 time to fit residues: 68.0081 Evaluate side-chains 274 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 194 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 216 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 161 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 272 optimal weight: 20.0000 chunk 51 optimal weight: 8.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 802 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.115620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.096233 restraints weight = 57790.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.097910 restraints weight = 41880.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.099068 restraints weight = 33576.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.099746 restraints weight = 28851.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.099886 restraints weight = 26109.542| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 24162 Z= 0.101 Angle : 0.538 7.910 32950 Z= 0.281 Chirality : 0.043 0.322 3858 Planarity : 0.004 0.061 4182 Dihedral : 4.625 35.547 3348 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.15), residues: 3128 helix: 0.76 (0.16), residues: 1188 sheet: -1.58 (0.27), residues: 424 loop : -1.54 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 712 TYR 0.008 0.001 TYR B 231 PHE 0.019 0.001 PHE D 671 TRP 0.019 0.001 TRP D 607 HIS 0.004 0.001 HIS B 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (24144) covalent geometry : angle 0.53627 / 0.28 (32912) SS BOND : bond 0.00377 / 0.24 ( 16) SS BOND : angle 1.63023 / 1.20 ( 32) hydrogen bonds : bond 0.03185 / 2.23 ( 848) hydrogen bonds : angle 4.40995 / 3.03 ( 2340) link_NAG-ASN : bond 0.00107 / 0.05 ( 2) link_NAG-ASN : angle 0.63828 / 0.29 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3266.63 seconds wall clock time: 57 minutes 25.63 seconds (3445.63 seconds total)