Starting phenix.real_space_refine on Thu Mar 5 16:32:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6whw_21678/03_2026/6whw_21678.cif Found real_map, /net/cci-nas-00/data/ceres_data/6whw_21678/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6whw_21678/03_2026/6whw_21678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6whw_21678/03_2026/6whw_21678.map" model { file = "/net/cci-nas-00/data/ceres_data/6whw_21678/03_2026/6whw_21678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6whw_21678/03_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-dev-5986/lib/python3.9/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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, D Time building chain proxies: 9.47, per 1000 atoms: 0.40 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: 2.11 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: 0.98 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: 4.90 Time building geometry restraints manager: 2.86 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: 12762 17.45 - 34.90: 1264 34.90 - 52.36: 196 52.36 - 69.81: 32 69.81 - 87.26: 34 Dihedral angle restraints: 14288 sinusoidal: 5142 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 14285 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: 0.04 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.280 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 26.360 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 : 14.558 87.258 8340 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 covalent geometry : bond 0.00904 (24144) covalent geometry : angle 0.86640 (32912) SS BOND : bond 0.01513 ( 16) SS BOND : angle 3.13350 ( 32) hydrogen bonds : bond 0.21845 ( 848) hydrogen bonds : angle 8.69224 ( 2340) link_NAG-ASN : bond 0.00403 ( 2) link_NAG-ASN : angle 0.87187 ( 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 : 0.900 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: 0.1371 time to fit residues: 76.0739 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 : 0.618 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 291 GLN 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: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.110803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.091783 restraints weight = 58269.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.093446 restraints weight = 41907.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.094605 restraints weight = 33478.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.095408 restraints weight = 28736.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.095857 restraints weight = 25836.753| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2002 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= 0.130 Angle : 0.629 7.876 32950 Z= 0.340 Chirality : 0.046 0.232 3858 Planarity : 0.005 0.073 4182 Dihedral : 6.319 46.683 3390 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.19 % Favored : 92.68 % Rotamer: Outliers : 0.25 % Allowed : 3.84 % Favored : 95.91 % 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: -3.27 (0.14), residues: 3128 helix: -1.09 (0.14), residues: 1198 sheet: -3.38 (0.21), residues: 402 loop : -2.72 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 367 TYR 0.014 0.001 TYR C 253 PHE 0.017 0.002 PHE D 474 TRP 0.013 0.001 TRP B 844 HIS 0.004 0.001 HIS B 802 Details of bonding type rmsd covalent geometry : bond 0.00287 (24144) covalent geometry : angle 0.62515 (32912) SS BOND : bond 0.00688 ( 16) SS BOND : angle 2.42732 ( 32) hydrogen bonds : bond 0.04603 ( 848) hydrogen bonds : angle 5.64602 ( 2340) link_NAG-ASN : bond 0.00074 ( 2) link_NAG-ASN : angle 0.53085 ( 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 356 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 350 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8163 (mmt) cc_final: 0.7947 (mmm) REVERT: A 149 SER cc_start: 0.7764 (m) cc_final: 0.7539 (t) REVERT: A 163 ILE cc_start: 0.8950 (pt) cc_final: 0.8748 (pt) REVERT: A 375 MET cc_start: 0.8082 (tpp) cc_final: 0.7626 (tpp) REVERT: A 774 PHE cc_start: 0.7547 (t80) cc_final: 0.7230 (t80) REVERT: B 94 ILE cc_start: 0.6780 (mm) cc_final: 0.6377 (mm) REVERT: B 127 HIS cc_start: 0.7077 (t70) cc_final: 0.6837 (t-170) REVERT: B 307 MET cc_start: 0.6811 (ttp) cc_final: 0.6095 (tmm) REVERT: B 473 LYS cc_start: 0.8945 (mtmm) cc_final: 0.8666 (mttp) REVERT: B 677 PHE cc_start: 0.8007 (t80) cc_final: 0.7519 (t80) REVERT: B 824 MET cc_start: 0.6164 (mmt) cc_final: 0.5909 (mmt) REVERT: C 149 SER cc_start: 0.7867 (m) cc_final: 0.7511 (t) REVERT: C 336 TRP cc_start: 0.7379 (t60) cc_final: 0.7131 (t60) REVERT: C 375 MET cc_start: 0.8028 (tpp) cc_final: 0.7773 (tpp) REVERT: C 686 THR cc_start: 0.8681 (p) cc_final: 0.8373 (t) REVERT: C 723 MET cc_start: 0.8592 (mtp) cc_final: 0.8225 (mtm) REVERT: D 307 MET cc_start: 0.6382 (ttp) cc_final: 0.6030 (tmm) REVERT: D 473 LYS cc_start: 0.8935 (mtmm) cc_final: 0.8666 (mttp) REVERT: D 677 PHE cc_start: 0.8018 (t80) cc_final: 0.7566 (t80) REVERT: D 824 MET cc_start: 0.5423 (mmt) cc_final: 0.4997 (mmm) outliers start: 6 outliers final: 2 residues processed: 356 average time/residue: 0.1323 time to fit residues: 77.5789 Evaluate side-chains 263 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 261 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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: 5.9990 chunk 279 optimal weight: 4.9990 chunk 119 optimal weight: 50.0000 chunk 295 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 289 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 197 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 156 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 HIS ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 ASN C 801 HIS ** D 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.108829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.089899 restraints weight = 58821.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.091432 restraints weight = 43388.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.092508 restraints weight = 35169.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.093245 restraints weight = 30413.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.093682 restraints weight = 27510.272| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 24162 Z= 0.204 Angle : 0.655 7.302 32950 Z= 0.350 Chirality : 0.046 0.243 3858 Planarity : 0.005 0.138 4182 Dihedral : 6.290 50.183 3390 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.07 % Favored : 89.83 % Rotamer: Outliers : 0.17 % Allowed : 4.92 % Favored : 94.92 % 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: -2.85 (0.14), residues: 3128 helix: -0.66 (0.15), residues: 1210 sheet: -3.38 (0.21), residues: 426 loop : -2.47 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 716 TYR 0.018 0.002 TYR C 253 PHE 0.022 0.002 PHE C 113 TRP 0.014 0.001 TRP B 607 HIS 0.007 0.001 HIS C 801 Details of bonding type rmsd covalent geometry : bond 0.00478 (24144) covalent geometry : angle 0.65051 (32912) SS BOND : bond 0.00520 ( 16) SS BOND : angle 2.58463 ( 32) hydrogen bonds : bond 0.04836 ( 848) hydrogen bonds : angle 5.54120 ( 2340) link_NAG-ASN : bond 0.00067 ( 2) link_NAG-ASN : angle 0.73223 ( 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 318 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 314 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8138 (mmt) cc_final: 0.7892 (mmm) REVERT: A 149 SER cc_start: 0.7940 (m) cc_final: 0.7592 (t) REVERT: A 336 TRP cc_start: 0.7479 (t60) cc_final: 0.7172 (t60) REVERT: A 375 MET cc_start: 0.8104 (tpp) cc_final: 0.7774 (tpp) REVERT: A 533 MET cc_start: 0.8023 (mtm) cc_final: 0.7818 (mtm) REVERT: B 94 ILE cc_start: 0.6874 (mm) cc_final: 0.6391 (mm) REVERT: B 134 MET cc_start: 0.8467 (mtp) cc_final: 0.8240 (mtp) REVERT: B 789 MET cc_start: 0.8339 (mtt) cc_final: 0.7930 (mtt) REVERT: B 824 MET cc_start: 0.6238 (mmt) cc_final: 0.6014 (mmt) REVERT: C 149 SER cc_start: 0.8069 (m) cc_final: 0.7760 (t) REVERT: C 686 THR cc_start: 0.8631 (p) cc_final: 0.8294 (t) REVERT: C 723 MET cc_start: 0.8581 (mtp) cc_final: 0.8246 (mtm) REVERT: D 73 MET cc_start: 0.7758 (ttm) cc_final: 0.7539 (ttm) REVERT: D 837 ILE cc_start: 0.7538 (mm) cc_final: 0.7271 (mt) outliers start: 4 outliers final: 0 residues processed: 318 average time/residue: 0.1315 time to fit residues: 69.1994 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 : 0.894 ------------------------------------------------------------------------------- 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: 10.0000 chunk 196 optimal weight: 7.9990 chunk 216 optimal weight: 0.6980 chunk 168 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 179 optimal weight: 0.0870 chunk 203 optimal weight: 0.6980 chunk 306 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 801 HIS ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 ASN ** D 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.113192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.094041 restraints weight = 58104.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.095722 restraints weight = 41932.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.096902 restraints weight = 33504.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.097748 restraints weight = 28675.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.098323 restraints weight = 25639.352| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 24162 Z= 0.109 Angle : 0.568 7.994 32950 Z= 0.304 Chirality : 0.044 0.238 3858 Planarity : 0.005 0.116 4182 Dihedral : 5.646 49.267 3390 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.91 % Favored : 93.00 % Rotamer: Outliers : 0.12 % Allowed : 2.40 % Favored : 97.48 % 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: -2.21 (0.15), residues: 3128 helix: -0.11 (0.15), residues: 1214 sheet: -2.90 (0.23), residues: 436 loop : -2.16 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 544 TYR 0.012 0.001 TYR C 668 PHE 0.017 0.001 PHE B 842 TRP 0.014 0.001 TRP B 607 HIS 0.006 0.001 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00242 (24144) covalent geometry : angle 0.56448 (32912) SS BOND : bond 0.00471 ( 16) SS BOND : angle 2.04056 ( 32) hydrogen bonds : bond 0.03772 ( 848) hydrogen bonds : angle 4.99410 ( 2340) link_NAG-ASN : bond 0.00065 ( 2) link_NAG-ASN : angle 0.60753 ( 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 352 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 349 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8051 (mmt) cc_final: 0.7818 (mmt) REVERT: A 149 SER cc_start: 0.7769 (m) cc_final: 0.7440 (t) REVERT: A 336 TRP cc_start: 0.7415 (t60) cc_final: 0.7023 (t60) REVERT: A 375 MET cc_start: 0.7830 (tpp) cc_final: 0.7539 (tpp) REVERT: A 585 LEU cc_start: 0.8754 (mm) cc_final: 0.8529 (mm) REVERT: A 834 MET cc_start: 0.8950 (mtp) cc_final: 0.8723 (mtp) REVERT: B 94 ILE cc_start: 0.6621 (mm) cc_final: 0.6187 (mm) REVERT: B 307 MET cc_start: 0.6702 (ttp) cc_final: 0.6060 (tmm) REVERT: B 677 PHE cc_start: 0.7879 (t80) cc_final: 0.7447 (t80) REVERT: B 777 ASP cc_start: 0.8269 (m-30) cc_final: 0.8030 (m-30) REVERT: B 824 MET cc_start: 0.6088 (mmt) cc_final: 0.5756 (mmp) REVERT: C 149 SER cc_start: 0.7951 (m) cc_final: 0.7665 (t) REVERT: C 686 THR cc_start: 0.8681 (p) cc_final: 0.8395 (t) REVERT: C 716 ARG cc_start: 0.7928 (ptm160) cc_final: 0.7633 (ptm160) REVERT: D 658 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7205 (mt-10) REVERT: D 677 PHE cc_start: 0.7855 (t80) cc_final: 0.7632 (t80) REVERT: D 777 ASP cc_start: 0.8211 (m-30) cc_final: 0.8005 (m-30) REVERT: D 824 MET cc_start: 0.5721 (mmt) cc_final: 0.5338 (mmm) REVERT: D 837 ILE cc_start: 0.7528 (mm) cc_final: 0.7263 (mt) outliers start: 3 outliers final: 0 residues processed: 351 average time/residue: 0.1327 time to fit residues: 77.0942 Evaluate side-chains 275 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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: 7.9990 chunk 87 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 224 optimal weight: 0.6980 chunk 100 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 260 optimal weight: 8.9990 chunk 305 optimal weight: 9.9990 chunk 173 optimal weight: 6.9990 chunk 280 optimal weight: 0.0770 chunk 118 optimal weight: 6.9990 overall best weight: 1.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 HIS ** 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 = 0.3519 r_free = 0.3519 target = 0.112249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.092908 restraints weight = 58244.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.094566 restraints weight = 42108.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.095724 restraints weight = 33736.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.096411 restraints weight = 28871.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.097087 restraints weight = 26108.421| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24162 Z= 0.125 Angle : 0.570 9.266 32950 Z= 0.303 Chirality : 0.044 0.330 3858 Planarity : 0.004 0.103 4182 Dihedral : 5.423 48.241 3390 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.83 % Favored : 92.14 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.15), residues: 3128 helix: 0.03 (0.15), residues: 1218 sheet: -2.65 (0.24), residues: 432 loop : -2.03 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 716 TYR 0.011 0.001 TYR C 114 PHE 0.037 0.002 PHE D 784 TRP 0.013 0.001 TRP D 607 HIS 0.007 0.001 HIS D 840 Details of bonding type rmsd covalent geometry : bond 0.00291 (24144) covalent geometry : angle 0.56626 (32912) SS BOND : bond 0.00459 ( 16) SS BOND : angle 2.05060 ( 32) hydrogen bonds : bond 0.03826 ( 848) hydrogen bonds : angle 4.88028 ( 2340) link_NAG-ASN : bond 0.00048 ( 2) link_NAG-ASN : angle 0.62602 ( 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 327 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 SER cc_start: 0.7784 (m) cc_final: 0.7450 (t) REVERT: A 336 TRP cc_start: 0.7449 (t60) cc_final: 0.7064 (t60) REVERT: A 375 MET cc_start: 0.7737 (tpp) cc_final: 0.7414 (tpp) REVERT: B 94 ILE cc_start: 0.6984 (mm) cc_final: 0.6581 (mm) REVERT: B 134 MET cc_start: 0.8243 (mtp) cc_final: 0.8000 (mtp) REVERT: B 307 MET cc_start: 0.6756 (ttp) cc_final: 0.6086 (tmm) REVERT: B 412 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7443 (tm-30) REVERT: B 615 ASN cc_start: 0.7176 (m-40) cc_final: 0.6405 (p0) REVERT: B 824 MET cc_start: 0.6087 (mmt) cc_final: 0.5732 (mmp) REVERT: C 149 SER cc_start: 0.7970 (m) cc_final: 0.7671 (t) REVERT: C 686 THR cc_start: 0.8727 (p) cc_final: 0.8393 (t) REVERT: C 774 PHE cc_start: 0.7309 (t80) cc_final: 0.7089 (t80) REVERT: D 412 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7408 (tm-30) REVERT: D 544 THR cc_start: 0.7738 (t) cc_final: 0.7508 (t) REVERT: D 824 MET cc_start: 0.5678 (mmt) cc_final: 0.5368 (mmm) REVERT: D 837 ILE cc_start: 0.7547 (mm) cc_final: 0.7278 (mt) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.1289 time to fit residues: 70.4207 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 : 0.640 ------------------------------------------------------------------------------- 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: 9.9990 chunk 58 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 274 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 250 optimal weight: 0.6980 chunk 312 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 592 HIS ** 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 = 0.3512 r_free = 0.3512 target = 0.111852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.092524 restraints weight = 58391.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.094125 restraints weight = 42458.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.095224 restraints weight = 34202.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.096062 restraints weight = 29469.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.096493 restraints weight = 26440.142| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24162 Z= 0.146 Angle : 0.592 9.734 32950 Z= 0.313 Chirality : 0.044 0.321 3858 Planarity : 0.004 0.107 4182 Dihedral : 5.399 47.695 3390 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.64 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % 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: -1.84 (0.15), residues: 3128 helix: 0.14 (0.15), residues: 1200 sheet: -2.55 (0.24), residues: 428 loop : -1.94 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.015 0.001 TYR C 114 PHE 0.027 0.002 PHE A 113 TRP 0.024 0.001 TRP C 632 HIS 0.008 0.001 HIS B 840 Details of bonding type rmsd covalent geometry : bond 0.00343 (24144) covalent geometry : angle 0.58827 (32912) SS BOND : bond 0.00469 ( 16) SS BOND : angle 2.27601 ( 32) hydrogen bonds : bond 0.03920 ( 848) hydrogen bonds : angle 4.87954 ( 2340) link_NAG-ASN : bond 0.00026 ( 2) link_NAG-ASN : angle 0.63336 ( 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 323 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.901 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 149 SER cc_start: 0.7832 (m) cc_final: 0.7515 (t) REVERT: A 336 TRP cc_start: 0.7302 (t60) cc_final: 0.7047 (t60) REVERT: A 375 MET cc_start: 0.7673 (tpp) cc_final: 0.7395 (tpp) REVERT: B 94 ILE cc_start: 0.6986 (mm) cc_final: 0.6651 (mm) REVERT: B 134 MET cc_start: 0.8311 (mtp) cc_final: 0.8097 (mtp) REVERT: B 824 MET cc_start: 0.6108 (mmt) cc_final: 0.5799 (mmp) REVERT: C 149 SER cc_start: 0.7968 (m) cc_final: 0.7681 (t) REVERT: C 585 LEU cc_start: 0.8814 (mm) cc_final: 0.8441 (mm) REVERT: C 628 MET cc_start: 0.8025 (mmm) cc_final: 0.7813 (mmm) REVERT: C 686 THR cc_start: 0.8721 (p) cc_final: 0.8405 (t) REVERT: D 412 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7315 (tm-30) outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.1223 time to fit residues: 66.4987 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 : 0.651 ------------------------------------------------------------------------------- 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: 20.0000 chunk 298 optimal weight: 8.9990 chunk 203 optimal weight: 2.9990 chunk 178 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 219 optimal weight: 5.9990 chunk 230 optimal weight: 0.4980 chunk 158 optimal weight: 8.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 HIS ** 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 = 0.3526 r_free = 0.3526 target = 0.112694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.093314 restraints weight = 58146.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.094961 restraints weight = 42353.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.096130 restraints weight = 34094.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.096943 restraints weight = 29236.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.097490 restraints weight = 26252.960| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24162 Z= 0.124 Angle : 0.572 10.467 32950 Z= 0.302 Chirality : 0.044 0.365 3858 Planarity : 0.004 0.101 4182 Dihedral : 5.210 45.919 3390 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.83 % Favored : 92.14 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: -1.67 (0.15), residues: 3128 helix: 0.26 (0.16), residues: 1206 sheet: -2.43 (0.24), residues: 444 loop : -1.82 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 716 TYR 0.017 0.001 TYR C 114 PHE 0.022 0.002 PHE C 113 TRP 0.013 0.001 TRP D 607 HIS 0.005 0.001 HIS B 840 Details of bonding type rmsd covalent geometry : bond 0.00290 (24144) covalent geometry : angle 0.56824 (32912) SS BOND : bond 0.00446 ( 16) SS BOND : angle 2.29698 ( 32) hydrogen bonds : bond 0.03687 ( 848) hydrogen bonds : angle 4.77729 ( 2340) link_NAG-ASN : bond 0.00042 ( 2) link_NAG-ASN : angle 0.63541 ( 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 319 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 SER cc_start: 0.7909 (m) cc_final: 0.7638 (t) REVERT: A 336 TRP cc_start: 0.7359 (t60) cc_final: 0.7113 (t60) REVERT: A 375 MET cc_start: 0.7661 (tpp) cc_final: 0.6906 (tpp) REVERT: B 94 ILE cc_start: 0.6823 (mm) cc_final: 0.6579 (mm) REVERT: B 307 MET cc_start: 0.6786 (ttp) cc_final: 0.6126 (tmm) REVERT: B 470 LYS cc_start: 0.8684 (mmmt) cc_final: 0.8450 (tppt) REVERT: B 544 THR cc_start: 0.7817 (t) cc_final: 0.7587 (t) REVERT: B 677 PHE cc_start: 0.7911 (t80) cc_final: 0.7630 (t80) REVERT: B 824 MET cc_start: 0.6147 (mmt) cc_final: 0.5834 (mmp) REVERT: C 149 SER cc_start: 0.7932 (m) cc_final: 0.7652 (t) REVERT: C 375 MET cc_start: 0.7539 (tpp) cc_final: 0.6801 (tpp) REVERT: C 585 LEU cc_start: 0.8793 (mm) cc_final: 0.8423 (mm) REVERT: C 628 MET cc_start: 0.8087 (mmm) cc_final: 0.7846 (mmm) REVERT: C 686 THR cc_start: 0.8649 (p) cc_final: 0.8367 (t) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.1237 time to fit residues: 67.1554 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 : 0.812 ------------------------------------------------------------------------------- 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: 1.9990 chunk 181 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 195 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 244 optimal weight: 0.0970 chunk 153 optimal weight: 6.9990 chunk 267 optimal weight: 1.9990 chunk 298 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 520 ASN B 127 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.113354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.094066 restraints weight = 57750.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.095728 restraints weight = 41793.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.096901 restraints weight = 33518.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.097585 restraints weight = 28708.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.098232 restraints weight = 25912.640| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 24162 Z= 0.119 Angle : 0.573 9.275 32950 Z= 0.304 Chirality : 0.044 0.427 3858 Planarity : 0.005 0.133 4182 Dihedral : 5.108 44.878 3390 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.03 % 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: -1.54 (0.15), residues: 3128 helix: 0.36 (0.16), residues: 1206 sheet: -2.10 (0.25), residues: 434 loop : -1.84 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 716 TYR 0.016 0.001 TYR C 114 PHE 0.021 0.001 PHE C 113 TRP 0.021 0.001 TRP A 632 HIS 0.004 0.001 HIS B 840 Details of bonding type rmsd covalent geometry : bond 0.00279 (24144) covalent geometry : angle 0.56954 (32912) SS BOND : bond 0.00387 ( 16) SS BOND : angle 2.05291 ( 32) hydrogen bonds : bond 0.03556 ( 848) hydrogen bonds : angle 4.67042 ( 2340) link_NAG-ASN : bond 0.00068 ( 2) link_NAG-ASN : angle 0.62609 ( 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 327 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 SER cc_start: 0.7936 (m) cc_final: 0.7670 (t) REVERT: A 336 TRP cc_start: 0.7291 (t60) cc_final: 0.7018 (t60) REVERT: A 375 MET cc_start: 0.7502 (tpp) cc_final: 0.6800 (tpp) REVERT: B 307 MET cc_start: 0.6773 (ttp) cc_final: 0.6099 (tmm) REVERT: B 641 ILE cc_start: 0.9529 (tp) cc_final: 0.9298 (tp) REVERT: B 824 MET cc_start: 0.6138 (mmt) cc_final: 0.5816 (mmp) REVERT: C 149 SER cc_start: 0.7970 (m) cc_final: 0.7689 (t) REVERT: C 336 TRP cc_start: 0.7157 (t60) cc_final: 0.6711 (t60) REVERT: C 375 MET cc_start: 0.7491 (tpp) cc_final: 0.6821 (tpp) REVERT: C 585 LEU cc_start: 0.8723 (mm) cc_final: 0.8335 (mm) REVERT: C 628 MET cc_start: 0.8096 (mmm) cc_final: 0.7869 (mmm) REVERT: C 686 THR cc_start: 0.8646 (p) cc_final: 0.8349 (t) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.1248 time to fit residues: 69.2762 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 : 0.745 ------------------------------------------------------------------------------- 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: 0.9990 chunk 224 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 248 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 240 optimal weight: 0.9990 chunk 161 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 592 HIS ** 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 = 0.3555 r_free = 0.3555 target = 0.114558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.095230 restraints weight = 57508.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.096915 restraints weight = 41612.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.097922 restraints weight = 33194.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.098882 restraints weight = 28660.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.099369 restraints weight = 25651.695| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 24162 Z= 0.104 Angle : 0.555 8.613 32950 Z= 0.293 Chirality : 0.043 0.392 3858 Planarity : 0.005 0.128 4182 Dihedral : 4.897 42.835 3390 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.03 % 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: -1.37 (0.15), residues: 3128 helix: 0.48 (0.16), residues: 1208 sheet: -2.04 (0.25), residues: 470 loop : -1.69 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 776 TYR 0.015 0.001 TYR A 114 PHE 0.019 0.001 PHE B 836 TRP 0.013 0.001 TRP D 607 HIS 0.005 0.001 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00241 (24144) covalent geometry : angle 0.55248 (32912) SS BOND : bond 0.00355 ( 16) SS BOND : angle 1.85837 ( 32) hydrogen bonds : bond 0.03293 ( 848) hydrogen bonds : angle 4.55658 ( 2340) link_NAG-ASN : bond 0.00097 ( 2) link_NAG-ASN : angle 0.62577 ( 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 328 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 SER cc_start: 0.7824 (m) cc_final: 0.7561 (t) REVERT: A 336 TRP cc_start: 0.7251 (t60) cc_final: 0.7021 (t60) REVERT: A 375 MET cc_start: 0.7432 (tpp) cc_final: 0.6754 (tpp) REVERT: A 585 LEU cc_start: 0.8632 (mm) cc_final: 0.8398 (mm) REVERT: B 94 ILE cc_start: 0.6444 (mm) cc_final: 0.6240 (mm) REVERT: B 307 MET cc_start: 0.6686 (ttp) cc_final: 0.6034 (tmm) REVERT: B 641 ILE cc_start: 0.9539 (tp) cc_final: 0.9288 (tp) REVERT: B 824 MET cc_start: 0.6101 (mmt) cc_final: 0.5718 (mmp) REVERT: B 837 ILE cc_start: 0.7099 (mm) cc_final: 0.6808 (mt) REVERT: C 149 SER cc_start: 0.7907 (m) cc_final: 0.7637 (t) REVERT: C 375 MET cc_start: 0.7460 (tpp) cc_final: 0.6836 (tpp) REVERT: C 585 LEU cc_start: 0.8703 (mm) cc_final: 0.8284 (mm) REVERT: C 628 MET cc_start: 0.8081 (mmm) cc_final: 0.7850 (mmm) REVERT: C 686 THR cc_start: 0.8654 (p) cc_final: 0.8376 (t) REVERT: C 716 ARG cc_start: 0.7627 (ptm160) cc_final: 0.7318 (ttt180) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.1233 time to fit residues: 68.9296 Evaluate side-chains 269 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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: 0.0030 chunk 293 optimal weight: 0.9990 chunk 140 optimal weight: 0.3980 chunk 63 optimal weight: 8.9990 chunk 188 optimal weight: 10.0000 chunk 219 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 307 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3572 r_free = 0.3572 target = 0.115822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.096288 restraints weight = 57876.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.098007 restraints weight = 41626.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.099224 restraints weight = 33166.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.100086 restraints weight = 28299.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.100540 restraints weight = 25337.617| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.081 24162 Z= 0.098 Angle : 0.551 8.728 32950 Z= 0.289 Chirality : 0.043 0.393 3858 Planarity : 0.004 0.119 4182 Dihedral : 4.693 40.145 3390 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.07 % 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: -1.18 (0.15), residues: 3128 helix: 0.57 (0.16), residues: 1214 sheet: -1.64 (0.27), residues: 422 loop : -1.66 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 776 TYR 0.014 0.001 TYR A 114 PHE 0.017 0.001 PHE B 836 TRP 0.014 0.001 TRP D 607 HIS 0.003 0.001 HIS C 162 Details of bonding type rmsd covalent geometry : bond 0.00225 (24144) covalent geometry : angle 0.54889 (32912) SS BOND : bond 0.00349 ( 16) SS BOND : angle 1.69451 ( 32) hydrogen bonds : bond 0.03086 ( 848) hydrogen bonds : angle 4.40228 ( 2340) link_NAG-ASN : bond 0.00108 ( 2) link_NAG-ASN : angle 0.65104 ( 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 329 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 SER cc_start: 0.7851 (m) cc_final: 0.7560 (t) REVERT: A 336 TRP cc_start: 0.7202 (t60) cc_final: 0.6958 (t60) REVERT: A 375 MET cc_start: 0.7423 (tpp) cc_final: 0.6823 (tpp) REVERT: A 768 VAL cc_start: 0.9310 (p) cc_final: 0.9050 (t) REVERT: B 63 SER cc_start: 0.7933 (m) cc_final: 0.7337 (p) REVERT: B 209 LEU cc_start: 0.8403 (mp) cc_final: 0.8133 (mp) REVERT: B 307 MET cc_start: 0.6573 (ttp) cc_final: 0.5995 (tmm) REVERT: B 641 ILE cc_start: 0.9555 (tp) cc_final: 0.9292 (tp) REVERT: B 824 MET cc_start: 0.6219 (mmt) cc_final: 0.5929 (mmp) REVERT: B 837 ILE cc_start: 0.7108 (mm) cc_final: 0.6813 (mt) REVERT: C 149 SER cc_start: 0.7958 (m) cc_final: 0.7684 (t) REVERT: C 155 MET cc_start: 0.8259 (mtt) cc_final: 0.7933 (mtt) REVERT: C 375 MET cc_start: 0.7337 (tpp) cc_final: 0.6764 (tpp) REVERT: C 585 LEU cc_start: 0.8676 (mm) cc_final: 0.8205 (mm) REVERT: C 628 MET cc_start: 0.8050 (mmm) cc_final: 0.7842 (mmm) REVERT: C 686 THR cc_start: 0.8648 (p) cc_final: 0.8370 (t) REVERT: C 716 ARG cc_start: 0.7650 (ptm160) cc_final: 0.7315 (ttt180) REVERT: C 768 VAL cc_start: 0.9314 (p) cc_final: 0.9080 (t) outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 0.1227 time to fit residues: 68.9300 Evaluate side-chains 267 residues out of total 2744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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: 2.9990 chunk 72 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 216 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 161 optimal weight: 0.9980 chunk 8 optimal weight: 0.1980 chunk 49 optimal weight: 0.9990 chunk 272 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.115856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.096370 restraints weight = 57988.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.098128 restraints weight = 41614.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.099346 restraints weight = 32937.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.100179 restraints weight = 28149.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.100673 restraints weight = 25246.319| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 24162 Z= 0.101 Angle : 0.552 8.193 32950 Z= 0.290 Chirality : 0.043 0.390 3858 Planarity : 0.004 0.114 4182 Dihedral : 4.604 38.448 3390 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.07 % 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: -1.08 (0.15), residues: 3128 helix: 0.61 (0.16), residues: 1210 sheet: -1.61 (0.27), residues: 426 loop : -1.55 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 776 TYR 0.014 0.001 TYR A 114 PHE 0.017 0.001 PHE B 836 TRP 0.012 0.001 TRP A 813 HIS 0.003 0.000 HIS C 162 Details of bonding type rmsd covalent geometry : bond 0.00233 (24144) covalent geometry : angle 0.54956 (32912) SS BOND : bond 0.00358 ( 16) SS BOND : angle 1.62235 ( 32) hydrogen bonds : bond 0.03154 ( 848) hydrogen bonds : angle 4.37835 ( 2340) link_NAG-ASN : bond 0.00105 ( 2) link_NAG-ASN : angle 0.64859 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3128.79 seconds wall clock time: 54 minutes 56.75 seconds (3296.75 seconds total)