Starting phenix.real_space_refine on Thu Nov 20 17:47:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e8b_31013/11_2025/7e8b_31013.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e8b_31013/11_2025/7e8b_31013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7e8b_31013/11_2025/7e8b_31013.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e8b_31013/11_2025/7e8b_31013.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7e8b_31013/11_2025/7e8b_31013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e8b_31013/11_2025/7e8b_31013.map" } resolution = 4.2 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 166 5.16 5 C 23614 2.51 5 N 6230 2.21 5 O 6822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36832 Number of models: 1 Model: "" Number of chains: 8 Chain: "L" Number of atoms: 6087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 6087 Classifications: {'peptide': 757} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 721} Chain: "K" Number of atoms: 6087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 6087 Classifications: {'peptide': 757} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 721} Chain: "B" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3122 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 14, 'TRANS': 373} Chain breaks: 2 Chain: "A" Number of atoms: 3120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3120 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 14, 'TRANS': 373} Chain breaks: 2 Chain: "J" Number of atoms: 6087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 6087 Classifications: {'peptide': 757} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 721} Chain: "I" Number of atoms: 6087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 6087 Classifications: {'peptide': 757} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 721} Chain: "D" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3122 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 14, 'TRANS': 373} Chain breaks: 2 Chain: "C" Number of atoms: 3120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3120 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 14, 'TRANS': 373} Chain breaks: 2 Time building chain proxies: 8.49, per 1000 atoms: 0.23 Number of scatterers: 36832 At special positions: 0 Unit cell: (171, 161, 208, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 166 16.00 O 6822 8.00 N 6230 7.00 C 23614 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS L 349 " - pdb=" SG CYS L 356 " distance=2.03 Simple disulfide: pdb=" SG CYS L 465 " - pdb=" SG CYS L 468 " distance=2.03 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 492 " distance=2.04 Simple disulfide: pdb=" SG CYS L 673 " - pdb=" SG CYS L 784 " distance=2.03 Simple disulfide: pdb=" SG CYS K 349 " - pdb=" SG CYS K 356 " distance=2.03 Simple disulfide: pdb=" SG CYS K 465 " - pdb=" SG CYS K 468 " distance=2.03 Simple disulfide: pdb=" SG CYS K 474 " - pdb=" SG CYS K 492 " distance=2.03 Simple disulfide: pdb=" SG CYS K 673 " - pdb=" SG CYS K 784 " distance=2.03 Simple disulfide: pdb=" SG CYS J 349 " - pdb=" SG CYS J 356 " distance=2.03 Simple disulfide: pdb=" SG CYS J 465 " - pdb=" SG CYS J 468 " distance=2.03 Simple disulfide: pdb=" SG CYS J 474 " - pdb=" SG CYS J 492 " distance=2.04 Simple disulfide: pdb=" SG CYS J 673 " - pdb=" SG CYS J 784 " distance=2.03 Simple disulfide: pdb=" SG CYS I 349 " - pdb=" SG CYS I 356 " distance=2.03 Simple disulfide: pdb=" SG CYS I 465 " - pdb=" SG CYS I 468 " distance=2.03 Simple disulfide: pdb=" SG CYS I 474 " - pdb=" SG CYS I 492 " distance=2.03 Simple disulfide: pdb=" SG CYS I 673 " - pdb=" SG CYS I 784 " 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 Time building additional restraints: 3.12 Conformation dependent library (CDL) restraints added in 1.5 seconds 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8648 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 56 sheets defined 37.4% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'L' and resid 32 through 56 Processing helix chain 'L' and resid 70 through 75 removed outlier: 3.945A pdb=" N LEU L 74 " --> pdb=" O THR L 70 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE L 75 " --> pdb=" O VAL L 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 70 through 75' Processing helix chain 'L' and resid 76 through 80 removed outlier: 3.604A pdb=" N PHE L 79 " --> pdb=" O SER L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 118 through 122 removed outlier: 4.240A pdb=" N LYS L 121 " --> pdb=" O GLU L 118 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE L 122 " --> pdb=" O GLY L 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 118 through 122' Processing helix chain 'L' and resid 228 through 234 Processing helix chain 'L' and resid 517 through 527 removed outlier: 4.012A pdb=" N ASN L 525 " --> pdb=" O LYS L 521 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG L 527 " --> pdb=" O ALA L 523 " (cutoff:3.500A) Processing helix chain 'L' and resid 582 through 591 Processing helix chain 'L' and resid 608 through 613 removed outlier: 3.635A pdb=" N GLU L 613 " --> pdb=" O LYS L 609 " (cutoff:3.500A) Processing helix chain 'L' and resid 619 through 632 Processing helix chain 'L' and resid 651 through 659 removed outlier: 3.629A pdb=" N LEU L 655 " --> pdb=" O TYR L 651 " (cutoff:3.500A) Processing helix chain 'L' and resid 682 through 686 Processing helix chain 'L' and resid 687 through 696 removed outlier: 4.157A pdb=" N ARG L 693 " --> pdb=" O ALA L 689 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR L 694 " --> pdb=" O PHE L 690 " (cutoff:3.500A) Processing helix chain 'L' and resid 735 through 749 Processing helix chain 'L' and resid 766 through 786 removed outlier: 3.503A pdb=" N LYS L 770 " --> pdb=" O SER L 766 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU L 783 " --> pdb=" O ASN L 779 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS L 784 " --> pdb=" O PHE L 780 " (cutoff:3.500A) Processing helix chain 'K' and resid 32 through 56 Processing helix chain 'K' and resid 71 through 80 removed outlier: 3.785A pdb=" N LEU K 74 " --> pdb=" O VAL K 71 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLU K 77 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASP K 78 " --> pdb=" O PHE K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 228 through 234 Processing helix chain 'K' and resid 517 through 527 Processing helix chain 'K' and resid 582 through 592 Processing helix chain 'K' and resid 607 through 612 Processing helix chain 'K' and resid 619 through 635 removed outlier: 3.518A pdb=" N LYS K 635 " --> pdb=" O ARG K 631 " (cutoff:3.500A) Processing helix chain 'K' and resid 651 through 659 Processing helix chain 'K' and resid 687 through 696 removed outlier: 3.847A pdb=" N ARG K 693 " --> pdb=" O ALA K 689 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR K 694 " --> pdb=" O PHE K 690 " (cutoff:3.500A) Processing helix chain 'K' and resid 709 through 713 removed outlier: 3.578A pdb=" N HIS K 712 " --> pdb=" O LYS K 709 " (cutoff:3.500A) Processing helix chain 'K' and resid 734 through 749 removed outlier: 4.152A pdb=" N THR K 738 " --> pdb=" O HIS K 734 " (cutoff:3.500A) Processing helix chain 'K' and resid 766 through 786 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 90 through 102 Processing helix chain 'B' and resid 114 through 122 removed outlier: 3.554A pdb=" N GLU B 118 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 146 Processing helix chain 'B' and resid 151 through 156 removed outlier: 4.032A pdb=" N ASP B 155 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 177 Processing helix chain 'B' and resid 181 through 205 Processing helix chain 'B' and resid 228 through 251 removed outlier: 3.638A pdb=" N ALA B 251 " --> pdb=" O ARG B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 260 through 282 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 287 through 296 removed outlier: 4.235A pdb=" N THR B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 305 removed outlier: 3.640A pdb=" N LYS B 302 " --> pdb=" O ARG B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 320 Processing helix chain 'B' and resid 320 through 347 Processing helix chain 'B' and resid 356 through 369 removed outlier: 3.735A pdb=" N THR B 369 " --> pdb=" O ILE B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 400 Processing helix chain 'B' and resid 401 through 434 removed outlier: 4.188A pdb=" N ASP B 420 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS B 421 " --> pdb=" O GLN B 417 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG B 434 " --> pdb=" O LEU B 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 88 through 101 removed outlier: 3.710A pdb=" N HIS A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 122 removed outlier: 3.736A pdb=" N TYR A 115 " --> pdb=" O CYS A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 129 removed outlier: 4.054A pdb=" N ILE A 128 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE A 129 " --> pdb=" O PRO A 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 125 through 129' Processing helix chain 'A' and resid 131 through 150 removed outlier: 4.414A pdb=" N ASP A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 153 No H-bonds generated for 'chain 'A' and resid 151 through 153' Processing helix chain 'A' and resid 167 through 177 Processing helix chain 'A' and resid 181 through 205 Processing helix chain 'A' and resid 227 through 250 removed outlier: 3.676A pdb=" N CYS A 231 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 260 through 282 Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 287 through 299 removed outlier: 4.428A pdb=" N THR A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 308 through 320 Processing helix chain 'A' and resid 320 through 345 Processing helix chain 'A' and resid 356 through 369 removed outlier: 3.836A pdb=" N THR A 369 " --> pdb=" O ILE A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 400 Processing helix chain 'A' and resid 401 through 436 Processing helix chain 'J' and resid 32 through 56 Processing helix chain 'J' and resid 70 through 75 removed outlier: 3.945A pdb=" N LEU J 74 " --> pdb=" O THR J 70 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE J 75 " --> pdb=" O VAL J 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 70 through 75' Processing helix chain 'J' and resid 76 through 80 removed outlier: 3.604A pdb=" N PHE J 79 " --> pdb=" O SER J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 122 removed outlier: 4.241A pdb=" N LYS J 121 " --> pdb=" O GLU J 118 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE J 122 " --> pdb=" O GLY J 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 118 through 122' Processing helix chain 'J' and resid 228 through 234 Processing helix chain 'J' and resid 517 through 527 removed outlier: 4.012A pdb=" N ASN J 525 " --> pdb=" O LYS J 521 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG J 527 " --> pdb=" O ALA J 523 " (cutoff:3.500A) Processing helix chain 'J' and resid 582 through 591 Processing helix chain 'J' and resid 608 through 613 removed outlier: 3.634A pdb=" N GLU J 613 " --> pdb=" O LYS J 609 " (cutoff:3.500A) Processing helix chain 'J' and resid 619 through 632 Processing helix chain 'J' and resid 651 through 659 removed outlier: 3.628A pdb=" N LEU J 655 " --> pdb=" O TYR J 651 " (cutoff:3.500A) Processing helix chain 'J' and resid 682 through 686 Processing helix chain 'J' and resid 687 through 696 removed outlier: 4.156A pdb=" N ARG J 693 " --> pdb=" O ALA J 689 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR J 694 " --> pdb=" O PHE J 690 " (cutoff:3.500A) Processing helix chain 'J' and resid 735 through 749 Processing helix chain 'J' and resid 766 through 786 removed outlier: 3.503A pdb=" N LYS J 770 " --> pdb=" O SER J 766 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU J 783 " --> pdb=" O ASN J 779 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS J 784 " --> pdb=" O PHE J 780 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 56 Processing helix chain 'I' and resid 71 through 80 removed outlier: 3.787A pdb=" N LEU I 74 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLU I 77 " --> pdb=" O LEU I 74 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASP I 78 " --> pdb=" O PHE I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 234 Processing helix chain 'I' and resid 517 through 527 Processing helix chain 'I' and resid 582 through 592 Processing helix chain 'I' and resid 607 through 612 Processing helix chain 'I' and resid 619 through 635 removed outlier: 3.519A pdb=" N LYS I 635 " --> pdb=" O ARG I 631 " (cutoff:3.500A) Processing helix chain 'I' and resid 651 through 659 Processing helix chain 'I' and resid 687 through 696 removed outlier: 3.845A pdb=" N ARG I 693 " --> pdb=" O ALA I 689 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR I 694 " --> pdb=" O PHE I 690 " (cutoff:3.500A) Processing helix chain 'I' and resid 709 through 713 removed outlier: 3.577A pdb=" N HIS I 712 " --> pdb=" O LYS I 709 " (cutoff:3.500A) Processing helix chain 'I' and resid 734 through 749 removed outlier: 4.152A pdb=" N THR I 738 " --> pdb=" O HIS I 734 " (cutoff:3.500A) Processing helix chain 'I' and resid 766 through 786 Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 71 through 75 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 114 through 122 removed outlier: 3.562A pdb=" N GLU D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 146 Processing helix chain 'D' and resid 151 through 156 removed outlier: 4.032A pdb=" N ASP D 155 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 177 Processing helix chain 'D' and resid 181 through 205 Processing helix chain 'D' and resid 228 through 251 removed outlier: 3.638A pdb=" N ALA D 251 " --> pdb=" O ARG D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 260 through 282 Proline residue: D 272 - end of helix Processing helix chain 'D' and resid 287 through 296 removed outlier: 4.236A pdb=" N THR D 291 " --> pdb=" O GLY D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 305 removed outlier: 3.644A pdb=" N LYS D 302 " --> pdb=" O ARG D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 320 Processing helix chain 'D' and resid 320 through 347 Processing helix chain 'D' and resid 356 through 369 removed outlier: 3.735A pdb=" N THR D 369 " --> pdb=" O ILE D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 400 Processing helix chain 'D' and resid 401 through 434 removed outlier: 4.186A pdb=" N ASP D 420 " --> pdb=" O ASN D 416 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS D 421 " --> pdb=" O GLN D 417 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG D 434 " --> pdb=" O LEU D 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 70 through 75 Processing helix chain 'C' and resid 88 through 101 removed outlier: 3.711A pdb=" N HIS C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 122 removed outlier: 3.736A pdb=" N TYR C 115 " --> pdb=" O CYS C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 129 removed outlier: 4.054A pdb=" N ILE C 128 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE C 129 " --> pdb=" O PRO C 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 125 through 129' Processing helix chain 'C' and resid 131 through 150 removed outlier: 4.414A pdb=" N ASP C 150 " --> pdb=" O GLU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 153 No H-bonds generated for 'chain 'C' and resid 151 through 153' Processing helix chain 'C' and resid 167 through 177 Processing helix chain 'C' and resid 181 through 205 Processing helix chain 'C' and resid 227 through 250 removed outlier: 3.674A pdb=" N CYS C 231 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE C 239 " --> pdb=" O ALA C 235 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 260 Processing helix chain 'C' and resid 260 through 282 Proline residue: C 272 - end of helix Processing helix chain 'C' and resid 287 through 299 removed outlier: 4.428A pdb=" N THR C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE C 295 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARG C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL C 297 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE C 298 " --> pdb=" O VAL C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 305 Processing helix chain 'C' and resid 308 through 320 Processing helix chain 'C' and resid 320 through 345 Processing helix chain 'C' and resid 356 through 369 removed outlier: 3.840A pdb=" N THR C 369 " --> pdb=" O ILE C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 400 Processing helix chain 'C' and resid 401 through 436 Processing sheet with id=AA1, first strand: chain 'L' and resid 88 through 90 removed outlier: 3.551A pdb=" N SER L 90 " --> pdb=" O GLU L 93 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU L 93 " --> pdb=" O SER L 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'L' and resid 103 through 107 removed outlier: 6.964A pdb=" N VAL L 103 " --> pdb=" O LEU L 116 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 129 through 132 Processing sheet with id=AA4, first strand: chain 'L' and resid 192 through 196 removed outlier: 3.679A pdb=" N TYR L 202 " --> pdb=" O ILE L 211 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE L 211 " --> pdb=" O TYR L 202 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 242 through 244 Processing sheet with id=AA6, first strand: chain 'L' and resid 263 through 266 Processing sheet with id=AA7, first strand: chain 'L' and resid 319 through 326 removed outlier: 5.611A pdb=" N ILE L 321 " --> pdb=" O LEU L 337 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU L 337 " --> pdb=" O ILE L 321 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N MET L 323 " --> pdb=" O THR L 335 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL L 343 " --> pdb=" O ASN L 338 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N SER L 344 " --> pdb=" O GLU L 361 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLU L 361 " --> pdb=" O SER L 344 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU L 346 " --> pdb=" O LYS L 359 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 384 through 389 Processing sheet with id=AA9, first strand: chain 'L' and resid 425 through 432 removed outlier: 5.189A pdb=" N ILE L 428 " --> pdb=" O LEU L 441 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU L 441 " --> pdb=" O ILE L 428 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS L 437 " --> pdb=" O ASP L 432 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 478 through 480 removed outlier: 6.421A pdb=" N VAL L 502 " --> pdb=" O ASP L 513 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASP L 513 " --> pdb=" O VAL L 502 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 531 through 534 removed outlier: 3.612A pdb=" N VAL L 595 " --> pdb=" O LEU L 549 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL L 596 " --> pdb=" O PRO L 561 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU L 563 " --> pdb=" O VAL L 596 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N CYS L 598 " --> pdb=" O LEU L 563 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL L 565 " --> pdb=" O CYS L 598 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N TYR L 560 " --> pdb=" O ARG L 643 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ALA L 645 " --> pdb=" O TYR L 560 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU L 562 " --> pdb=" O ALA L 645 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N PHE L 647 " --> pdb=" O LEU L 562 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU L 564 " --> pdb=" O PHE L 647 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N CYS L 673 " --> pdb=" O THR L 642 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL L 644 " --> pdb=" O CYS L 673 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N SER L 675 " --> pdb=" O VAL L 644 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VAL L 646 " --> pdb=" O SER L 675 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N LEU L 677 " --> pdb=" O VAL L 646 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY L 674 " --> pdb=" O LEU L 723 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ILE L 725 " --> pdb=" O GLY L 674 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA L 676 " --> pdb=" O ILE L 725 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N GLN L 755 " --> pdb=" O PHE L 722 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE L 724 " --> pdb=" O GLN L 755 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N TYR L 757 " --> pdb=" O ILE L 724 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N HIS L 726 " --> pdb=" O TYR L 757 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 537 through 539 Processing sheet with id=AB4, first strand: chain 'K' and resid 88 through 90 removed outlier: 3.552A pdb=" N GLU K 93 " --> pdb=" O SER K 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 103 through 107 removed outlier: 6.851A pdb=" N VAL K 103 " --> pdb=" O LEU K 116 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR K 112 " --> pdb=" O ASN K 107 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 129 through 132 Processing sheet with id=AB7, first strand: chain 'K' and resid 192 through 195 removed outlier: 7.240A pdb=" N ILE K 200 " --> pdb=" O VAL K 213 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL K 213 " --> pdb=" O ILE K 200 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 222 through 224 Processing sheet with id=AB9, first strand: chain 'K' and resid 222 through 224 Processing sheet with id=AC1, first strand: chain 'K' and resid 263 through 266 Processing sheet with id=AC2, first strand: chain 'K' and resid 319 through 325 removed outlier: 5.646A pdb=" N ILE K 321 " --> pdb=" O LEU K 337 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU K 337 " --> pdb=" O ILE K 321 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET K 323 " --> pdb=" O THR K 335 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL K 343 " --> pdb=" O ASN K 338 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LEU K 348 " --> pdb=" O LYS K 358 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N LYS K 358 " --> pdb=" O LEU K 348 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ASP K 350 " --> pdb=" O CYS K 356 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N CYS K 356 " --> pdb=" O ASP K 350 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 384 through 389 Processing sheet with id=AC4, first strand: chain 'K' and resid 425 through 431 removed outlier: 7.192A pdb=" N VAL K 425 " --> pdb=" O THR K 443 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR K 443 " --> pdb=" O VAL K 425 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TYR K 439 " --> pdb=" O LEU K 429 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLU K 444 " --> pdb=" O ARG K 449 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N ARG K 449 " --> pdb=" O GLU K 444 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 478 through 481 removed outlier: 6.804A pdb=" N VAL K 502 " --> pdb=" O ASP K 513 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASP K 513 " --> pdb=" O VAL K 502 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 531 through 533 removed outlier: 3.584A pdb=" N VAL K 595 " --> pdb=" O LEU K 549 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N CYS K 598 " --> pdb=" O VAL K 565 " (cutoff:3.500A) removed outlier: 10.417A pdb=" N TYR K 560 " --> pdb=" O ARG K 641 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ARG K 643 " --> pdb=" O TYR K 560 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N CYS K 673 " --> pdb=" O VAL K 644 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL K 646 " --> pdb=" O CYS K 673 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 537 through 539 Processing sheet with id=AC8, first strand: chain 'K' and resid 676 through 677 removed outlier: 6.445A pdb=" N ALA K 676 " --> pdb=" O ILE K 725 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 51 through 55 removed outlier: 3.624A pdb=" N TYR B 83 " --> pdb=" O VAL B 44 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AD2, first strand: chain 'J' and resid 88 through 90 removed outlier: 3.551A pdb=" N SER J 90 " --> pdb=" O GLU J 93 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU J 93 " --> pdb=" O SER J 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'J' and resid 103 through 107 removed outlier: 6.964A pdb=" N VAL J 103 " --> pdb=" O LEU J 116 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 129 through 132 Processing sheet with id=AD5, first strand: chain 'J' and resid 192 through 196 removed outlier: 3.678A pdb=" N TYR J 202 " --> pdb=" O ILE J 211 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE J 211 " --> pdb=" O TYR J 202 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 242 through 244 Processing sheet with id=AD7, first strand: chain 'J' and resid 263 through 266 Processing sheet with id=AD8, first strand: chain 'J' and resid 319 through 326 removed outlier: 5.612A pdb=" N ILE J 321 " --> pdb=" O LEU J 337 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU J 337 " --> pdb=" O ILE J 321 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N MET J 323 " --> pdb=" O THR J 335 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL J 343 " --> pdb=" O ASN J 338 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N SER J 344 " --> pdb=" O GLU J 361 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLU J 361 " --> pdb=" O SER J 344 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU J 346 " --> pdb=" O LYS J 359 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 384 through 389 Processing sheet with id=AE1, first strand: chain 'J' and resid 425 through 432 removed outlier: 5.189A pdb=" N ILE J 428 " --> pdb=" O LEU J 441 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU J 441 " --> pdb=" O ILE J 428 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS J 437 " --> pdb=" O ASP J 432 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 478 through 480 removed outlier: 6.422A pdb=" N VAL J 502 " --> pdb=" O ASP J 513 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASP J 513 " --> pdb=" O VAL J 502 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 531 through 534 removed outlier: 3.615A pdb=" N VAL J 595 " --> pdb=" O LEU J 549 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N VAL J 596 " --> pdb=" O PRO J 561 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU J 563 " --> pdb=" O VAL J 596 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N CYS J 598 " --> pdb=" O LEU J 563 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL J 565 " --> pdb=" O CYS J 598 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N TYR J 560 " --> pdb=" O ARG J 643 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ALA J 645 " --> pdb=" O TYR J 560 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU J 562 " --> pdb=" O ALA J 645 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N PHE J 647 " --> pdb=" O LEU J 562 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU J 564 " --> pdb=" O PHE J 647 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N CYS J 673 " --> pdb=" O THR J 642 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL J 644 " --> pdb=" O CYS J 673 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N SER J 675 " --> pdb=" O VAL J 644 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VAL J 646 " --> pdb=" O SER J 675 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N LEU J 677 " --> pdb=" O VAL J 646 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLY J 674 " --> pdb=" O LEU J 723 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N ILE J 725 " --> pdb=" O GLY J 674 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA J 676 " --> pdb=" O ILE J 725 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N GLN J 755 " --> pdb=" O PHE J 722 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE J 724 " --> pdb=" O GLN J 755 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N TYR J 757 " --> pdb=" O ILE J 724 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N HIS J 726 " --> pdb=" O TYR J 757 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 537 through 539 Processing sheet with id=AE5, first strand: chain 'I' and resid 88 through 90 removed outlier: 3.557A pdb=" N GLU I 93 " --> pdb=" O SER I 90 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 103 through 107 removed outlier: 6.852A pdb=" N VAL I 103 " --> pdb=" O LEU I 116 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR I 112 " --> pdb=" O ASN I 107 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 129 through 132 Processing sheet with id=AE8, first strand: chain 'I' and resid 192 through 195 removed outlier: 7.239A pdb=" N ILE I 200 " --> pdb=" O VAL I 213 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL I 213 " --> pdb=" O ILE I 200 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 222 through 224 Processing sheet with id=AF1, first strand: chain 'I' and resid 222 through 224 Processing sheet with id=AF2, first strand: chain 'I' and resid 263 through 266 Processing sheet with id=AF3, first strand: chain 'I' and resid 319 through 325 removed outlier: 5.649A pdb=" N ILE I 321 " --> pdb=" O LEU I 337 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU I 337 " --> pdb=" O ILE I 321 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET I 323 " --> pdb=" O THR I 335 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N VAL I 343 " --> pdb=" O ASN I 338 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N LEU I 348 " --> pdb=" O LYS I 358 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LYS I 358 " --> pdb=" O LEU I 348 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ASP I 350 " --> pdb=" O CYS I 356 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N CYS I 356 " --> pdb=" O ASP I 350 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 384 through 389 Processing sheet with id=AF5, first strand: chain 'I' and resid 425 through 431 removed outlier: 7.300A pdb=" N VAL I 425 " --> pdb=" O THR I 443 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR I 443 " --> pdb=" O VAL I 425 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TYR I 439 " --> pdb=" O LEU I 429 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N GLU I 444 " --> pdb=" O ARG I 449 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N ARG I 449 " --> pdb=" O GLU I 444 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 478 through 481 removed outlier: 6.804A pdb=" N VAL I 502 " --> pdb=" O ASP I 513 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASP I 513 " --> pdb=" O VAL I 502 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 531 through 533 removed outlier: 3.591A pdb=" N VAL I 595 " --> pdb=" O LEU I 549 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N CYS I 598 " --> pdb=" O VAL I 565 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N TYR I 560 " --> pdb=" O ARG I 643 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ALA I 645 " --> pdb=" O TYR I 560 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU I 562 " --> pdb=" O ALA I 645 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N PHE I 647 " --> pdb=" O LEU I 562 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU I 564 " --> pdb=" O PHE I 647 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS I 673 " --> pdb=" O VAL I 644 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL I 646 " --> pdb=" O CYS I 673 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 537 through 539 Processing sheet with id=AF9, first strand: chain 'I' and resid 676 through 677 removed outlier: 6.448A pdb=" N ALA I 676 " --> pdb=" O ILE I 725 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 51 through 55 removed outlier: 3.613A pdb=" N TYR D 83 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 45 through 46 1531 hydrogen bonds defined for protein. 4275 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: 8.48 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11830 1.34 - 1.46: 9096 1.46 - 1.58: 16562 1.58 - 1.70: 0 1.70 - 1.82: 256 Bond restraints: 37744 Sorted by residual: bond pdb=" CB PRO C 126 " pdb=" CG PRO C 126 " ideal model delta sigma weight residual 1.492 1.574 -0.082 5.00e-02 4.00e+02 2.72e+00 bond pdb=" CB PRO A 126 " pdb=" CG PRO A 126 " ideal model delta sigma weight residual 1.492 1.573 -0.081 5.00e-02 4.00e+02 2.65e+00 bond pdb=" CG PRO A 126 " pdb=" CD PRO A 126 " ideal model delta sigma weight residual 1.503 1.448 0.055 3.40e-02 8.65e+02 2.62e+00 bond pdb=" CG PRO C 126 " pdb=" CD PRO C 126 " ideal model delta sigma weight residual 1.503 1.449 0.054 3.40e-02 8.65e+02 2.54e+00 bond pdb=" C ILE K 162 " pdb=" N PRO K 163 " ideal model delta sigma weight residual 1.334 1.369 -0.036 2.34e-02 1.83e+03 2.31e+00 ... (remaining 37739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 50339 1.97 - 3.93: 727 3.93 - 5.90: 90 5.90 - 7.86: 24 7.86 - 9.83: 10 Bond angle restraints: 51190 Sorted by residual: angle pdb=" CA PRO A 126 " pdb=" N PRO A 126 " pdb=" CD PRO A 126 " ideal model delta sigma weight residual 112.00 105.45 6.55 1.40e+00 5.10e-01 2.19e+01 angle pdb=" CA PRO C 126 " pdb=" N PRO C 126 " pdb=" CD PRO C 126 " ideal model delta sigma weight residual 112.00 105.49 6.51 1.40e+00 5.10e-01 2.16e+01 angle pdb=" N PRO C 126 " pdb=" CD PRO C 126 " pdb=" CG PRO C 126 " ideal model delta sigma weight residual 103.20 96.45 6.75 1.50e+00 4.44e-01 2.03e+01 angle pdb=" N PRO A 126 " pdb=" CD PRO A 126 " pdb=" CG PRO A 126 " ideal model delta sigma weight residual 103.20 96.48 6.72 1.50e+00 4.44e-01 2.01e+01 angle pdb=" C GLU D 283 " pdb=" CA GLU D 283 " pdb=" CB GLU D 283 " ideal model delta sigma weight residual 115.79 110.95 4.84 1.19e+00 7.06e-01 1.65e+01 ... (remaining 51185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 20201 17.77 - 35.54: 1835 35.54 - 53.31: 370 53.31 - 71.08: 43 71.08 - 88.85: 41 Dihedral angle restraints: 22490 sinusoidal: 9042 harmonic: 13448 Sorted by residual: dihedral pdb=" CB CYS J 465 " pdb=" SG CYS J 465 " pdb=" SG CYS J 468 " pdb=" CB CYS J 468 " ideal model delta sinusoidal sigma weight residual 93.00 16.39 76.61 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CB CYS L 465 " pdb=" SG CYS L 465 " pdb=" SG CYS L 468 " pdb=" CB CYS L 468 " ideal model delta sinusoidal sigma weight residual 93.00 16.40 76.60 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CB CYS J 474 " pdb=" SG CYS J 474 " pdb=" SG CYS J 492 " pdb=" CB CYS J 492 " ideal model delta sinusoidal sigma weight residual -86.00 -22.03 -63.97 1 1.00e+01 1.00e-02 5.39e+01 ... (remaining 22487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3988 0.040 - 0.081: 1193 0.081 - 0.121: 414 0.121 - 0.162: 49 0.162 - 0.202: 8 Chirality restraints: 5652 Sorted by residual: chirality pdb=" CB ILE J 659 " pdb=" CA ILE J 659 " pdb=" CG1 ILE J 659 " pdb=" CG2 ILE J 659 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB ILE L 659 " pdb=" CA ILE L 659 " pdb=" CG1 ILE L 659 " pdb=" CG2 ILE L 659 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.20 2.00e-01 2.50e+01 9.88e-01 chirality pdb=" CA LEU A 400 " pdb=" N LEU A 400 " pdb=" C LEU A 400 " pdb=" CB LEU A 400 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.77e-01 ... (remaining 5649 not shown) Planarity restraints: 6526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 400 " -0.065 5.00e-02 4.00e+02 9.88e-02 1.56e+01 pdb=" N PRO C 401 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO C 401 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 401 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 400 " 0.065 5.00e-02 4.00e+02 9.88e-02 1.56e+01 pdb=" N PRO A 401 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO A 401 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 401 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 235 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C ALA D 235 " 0.032 2.00e-02 2.50e+03 pdb=" O ALA D 235 " -0.012 2.00e-02 2.50e+03 pdb=" N CYS D 236 " -0.011 2.00e-02 2.50e+03 ... (remaining 6523 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 913 2.68 - 3.23: 37815 3.23 - 3.79: 59790 3.79 - 4.34: 79335 4.34 - 4.90: 126316 Nonbonded interactions: 304169 Sorted by model distance: nonbonded pdb=" OE2 GLU C 346 " pdb=" OG1 THR C 380 " model vdw 2.120 3.040 nonbonded pdb=" OE2 GLU A 346 " pdb=" OG1 THR A 380 " model vdw 2.120 3.040 nonbonded pdb=" OD1 ASP D 116 " pdb=" OH TYR D 137 " model vdw 2.157 3.040 nonbonded pdb=" OD1 ASP B 116 " pdb=" OH TYR B 137 " model vdw 2.157 3.040 nonbonded pdb=" OH TYR I 96 " pdb=" OE1 GLN I 99 " model vdw 2.188 3.040 ... (remaining 304164 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 40 through 158 or resid 167 through 436)) selection = (chain 'B' and (resid 40 through 158 or resid 167 through 436)) selection = (chain 'C' and (resid 40 through 158 or resid 167 through 436)) selection = (chain 'D' and (resid 40 through 158 or resid 167 through 436)) } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 2.380 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: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 34.530 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 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 : 0.003 0.082 37760 Z= 0.123 Angle : 0.608 9.825 51222 Z= 0.324 Chirality : 0.044 0.202 5652 Planarity : 0.004 0.099 6526 Dihedral : 14.233 88.849 13794 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.26 % Favored : 92.70 % Rotamer: Outliers : 0.05 % Allowed : 0.42 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.12), residues: 4548 helix: 0.44 (0.14), residues: 1566 sheet: -0.48 (0.18), residues: 778 loop : -1.68 (0.13), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 388 TYR 0.031 0.001 TYR B 363 PHE 0.018 0.001 PHE J 385 TRP 0.020 0.001 TRP I 583 HIS 0.016 0.001 HIS D 414 Details of bonding type rmsd covalent geometry : bond 0.00260 (37744) covalent geometry : angle 0.60599 (51190) SS BOND : bond 0.00260 ( 16) SS BOND : angle 1.93497 ( 32) hydrogen bonds : bond 0.15529 ( 1527) hydrogen bonds : angle 6.70230 ( 4275) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 4028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 572 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 323 MET cc_start: 0.5094 (tmm) cc_final: 0.4722 (tmm) REVERT: L 424 ASP cc_start: 0.4710 (m-30) cc_final: 0.4433 (m-30) REVERT: L 475 THR cc_start: 0.6310 (p) cc_final: 0.5566 (p) REVERT: L 546 MET cc_start: 0.3925 (tmm) cc_final: 0.3500 (tmm) REVERT: L 609 LYS cc_start: 0.5489 (tptp) cc_final: 0.5016 (tppp) REVERT: L 641 ARG cc_start: 0.6026 (mpt-90) cc_final: 0.4094 (mtm180) REVERT: L 658 TYR cc_start: 0.6181 (t80) cc_final: 0.5734 (t80) REVERT: K 488 PHE cc_start: 0.6638 (p90) cc_final: 0.6410 (p90) REVERT: K 650 ASP cc_start: 0.8293 (m-30) cc_final: 0.7986 (m-30) REVERT: B 64 ASP cc_start: 0.5618 (p0) cc_final: 0.5310 (m-30) REVERT: B 98 PHE cc_start: 0.6129 (t80) cc_final: 0.5674 (t80) REVERT: B 279 MET cc_start: 0.7648 (tmm) cc_final: 0.7273 (tpp) REVERT: A 115 TYR cc_start: 0.5775 (t80) cc_final: 0.5503 (t80) REVERT: A 137 TYR cc_start: 0.6147 (t80) cc_final: 0.5730 (t80) REVERT: A 306 HIS cc_start: 0.6754 (m90) cc_final: 0.5871 (t70) REVERT: J 323 MET cc_start: 0.5085 (tmm) cc_final: 0.4713 (tmm) REVERT: J 424 ASP cc_start: 0.4726 (m-30) cc_final: 0.4450 (m-30) REVERT: J 475 THR cc_start: 0.6385 (p) cc_final: 0.5674 (p) REVERT: J 546 MET cc_start: 0.4068 (tmm) cc_final: 0.3796 (tmm) REVERT: J 609 LYS cc_start: 0.5485 (tptp) cc_final: 0.5010 (tppp) REVERT: J 641 ARG cc_start: 0.6024 (mpt-90) cc_final: 0.4095 (mtm180) REVERT: J 657 THR cc_start: 0.8140 (p) cc_final: 0.7932 (p) REVERT: J 658 TYR cc_start: 0.6166 (t80) cc_final: 0.5718 (t80) REVERT: I 488 PHE cc_start: 0.6604 (p90) cc_final: 0.6354 (p90) REVERT: I 650 ASP cc_start: 0.8284 (m-30) cc_final: 0.7976 (m-30) REVERT: D 64 ASP cc_start: 0.5663 (p0) cc_final: 0.5366 (m-30) REVERT: D 98 PHE cc_start: 0.6104 (t80) cc_final: 0.5662 (t80) REVERT: D 279 MET cc_start: 0.7626 (tmm) cc_final: 0.7256 (tpp) REVERT: C 115 TYR cc_start: 0.5760 (t80) cc_final: 0.5486 (t80) REVERT: C 137 TYR cc_start: 0.6124 (t80) cc_final: 0.5701 (t80) REVERT: C 306 HIS cc_start: 0.6781 (m90) cc_final: 0.5882 (t70) outliers start: 2 outliers final: 0 residues processed: 574 average time/residue: 0.2326 time to fit residues: 217.3878 Evaluate side-chains 325 residues out of total 4028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.0980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 1.9990 chunk 424 optimal weight: 0.8980 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 144 ASN ** K 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 416 GLN K 451 GLN K 547 GLN ** K 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 698 HIS K 762 HIS B 144 ASN B 202 ASN B 414 HIS ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 169 GLN I 144 ASN ** I 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 416 GLN I 451 GLN I 547 GLN ** I 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 698 HIS I 762 HIS D 144 ASN D 202 ASN D 414 HIS ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.111097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.095311 restraints weight = 155384.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.094576 restraints weight = 197166.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.094115 restraints weight = 148803.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.094048 restraints weight = 136655.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.094139 restraints weight = 124796.645| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 37760 Z= 0.192 Angle : 0.647 10.033 51222 Z= 0.344 Chirality : 0.046 0.158 5652 Planarity : 0.005 0.064 6526 Dihedral : 4.678 22.576 5064 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.92 % Favored : 92.04 % Rotamer: Outliers : 0.15 % Allowed : 6.93 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.23 (0.12), residues: 4548 helix: 0.43 (0.13), residues: 1618 sheet: -0.81 (0.18), residues: 802 loop : -1.82 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 449 TYR 0.016 0.002 TYR D 188 PHE 0.026 0.002 PHE I 722 TRP 0.013 0.002 TRP J 244 HIS 0.009 0.001 HIS J 612 Details of bonding type rmsd covalent geometry : bond 0.00431 (37744) covalent geometry : angle 0.64609 (51190) SS BOND : bond 0.00288 ( 16) SS BOND : angle 1.35270 ( 32) hydrogen bonds : bond 0.04757 ( 1527) hydrogen bonds : angle 5.58294 ( 4275) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 4028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 417 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 309 MET cc_start: 0.6969 (tpp) cc_final: 0.6579 (tpp) REVERT: L 546 MET cc_start: 0.4194 (tmm) cc_final: 0.3894 (tmm) REVERT: L 609 LYS cc_start: 0.5561 (tptp) cc_final: 0.5256 (tppp) REVERT: L 641 ARG cc_start: 0.6063 (mpt-90) cc_final: 0.4128 (mtm180) REVERT: L 657 THR cc_start: 0.8147 (p) cc_final: 0.7909 (p) REVERT: K 698 HIS cc_start: 0.5300 (OUTLIER) cc_final: 0.4796 (t70) REVERT: B 64 ASP cc_start: 0.5327 (p0) cc_final: 0.5113 (m-30) REVERT: B 247 ARG cc_start: 0.6950 (mmt90) cc_final: 0.6592 (mmm-85) REVERT: B 279 MET cc_start: 0.7323 (tmm) cc_final: 0.7123 (tpp) REVERT: B 368 MET cc_start: 0.8094 (mtp) cc_final: 0.7664 (mtp) REVERT: A 306 HIS cc_start: 0.6520 (m90) cc_final: 0.5734 (t70) REVERT: J 309 MET cc_start: 0.6968 (tpp) cc_final: 0.6574 (tpp) REVERT: J 546 MET cc_start: 0.4193 (tmm) cc_final: 0.3898 (tmm) REVERT: J 609 LYS cc_start: 0.5568 (tptp) cc_final: 0.5259 (tppp) REVERT: J 641 ARG cc_start: 0.6052 (mpt-90) cc_final: 0.4122 (mtm180) REVERT: J 657 THR cc_start: 0.8142 (p) cc_final: 0.7908 (p) REVERT: I 698 HIS cc_start: 0.5272 (OUTLIER) cc_final: 0.4818 (t70) REVERT: D 64 ASP cc_start: 0.5387 (p0) cc_final: 0.5177 (m-30) REVERT: D 247 ARG cc_start: 0.6949 (mmt90) cc_final: 0.6582 (mmm-85) REVERT: D 368 MET cc_start: 0.8026 (mtp) cc_final: 0.7627 (mtp) REVERT: C 306 HIS cc_start: 0.6532 (m90) cc_final: 0.5736 (t70) outliers start: 6 outliers final: 0 residues processed: 421 average time/residue: 0.2271 time to fit residues: 158.5640 Evaluate side-chains 297 residues out of total 4028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 295 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 3 optimal weight: 7.9990 chunk 147 optimal weight: 0.7980 chunk 134 optimal weight: 9.9990 chunk 133 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 363 optimal weight: 0.9980 chunk 340 optimal weight: 1.9990 chunk 325 optimal weight: 0.1980 chunk 345 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 9 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 667 GLN K 82 HIS K 209 GLN K 304 HIS ** K 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 416 GLN B 56 GLN B 416 ASN ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN J 606 GLN J 667 GLN I 82 HIS I 209 GLN I 304 HIS ** I 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 416 GLN D 56 GLN D 416 ASN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.112937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.097317 restraints weight = 154574.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.097918 restraints weight = 203144.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.098992 restraints weight = 163746.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.099011 restraints weight = 121365.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.099463 restraints weight = 106573.028| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37760 Z= 0.123 Angle : 0.580 7.070 51222 Z= 0.306 Chirality : 0.044 0.155 5652 Planarity : 0.004 0.068 6526 Dihedral : 4.502 20.950 5064 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.06 (0.12), residues: 4548 helix: 0.66 (0.13), residues: 1584 sheet: -0.72 (0.18), residues: 812 loop : -1.76 (0.13), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 142 TYR 0.015 0.001 TYR J 149 PHE 0.022 0.001 PHE C 187 TRP 0.010 0.001 TRP L 244 HIS 0.008 0.001 HIS I 304 Details of bonding type rmsd covalent geometry : bond 0.00261 (37744) covalent geometry : angle 0.57948 (51190) SS BOND : bond 0.00333 ( 16) SS BOND : angle 1.14683 ( 32) hydrogen bonds : bond 0.04336 ( 1527) hydrogen bonds : angle 5.27543 ( 4275) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 4028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 462 time to evaluate : 1.611 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: L 38 LEU cc_start: 0.7801 (tp) cc_final: 0.7579 (tp) REVERT: L 44 ILE cc_start: 0.7915 (mt) cc_final: 0.7625 (mt) REVERT: L 240 ILE cc_start: 0.6069 (mm) cc_final: 0.5569 (pt) REVERT: L 609 LYS cc_start: 0.5618 (tptp) cc_final: 0.5324 (tppp) REVERT: L 641 ARG cc_start: 0.6134 (mpt-90) cc_final: 0.4222 (mtm180) REVERT: B 64 ASP cc_start: 0.5410 (p0) cc_final: 0.5208 (m-30) REVERT: B 148 LEU cc_start: 0.8660 (mp) cc_final: 0.8035 (tt) REVERT: B 247 ARG cc_start: 0.6938 (mmt90) cc_final: 0.6486 (mmm-85) REVERT: B 368 MET cc_start: 0.8063 (mtp) cc_final: 0.7756 (mtp) REVERT: B 422 ARG cc_start: 0.6700 (pmt-80) cc_final: 0.6337 (ptm160) REVERT: A 137 TYR cc_start: 0.5824 (t80) cc_final: 0.5449 (t80) REVERT: A 306 HIS cc_start: 0.6249 (m90) cc_final: 0.5638 (t70) REVERT: A 389 ILE cc_start: 0.9173 (mt) cc_final: 0.8922 (mm) REVERT: J 38 LEU cc_start: 0.7796 (tp) cc_final: 0.7580 (tp) REVERT: J 44 ILE cc_start: 0.7920 (mt) cc_final: 0.7624 (mt) REVERT: J 240 ILE cc_start: 0.6057 (mm) cc_final: 0.5577 (pt) REVERT: J 424 ASP cc_start: 0.4964 (m-30) cc_final: 0.4536 (m-30) REVERT: J 546 MET cc_start: 0.4285 (tmm) cc_final: 0.3852 (tmm) REVERT: J 609 LYS cc_start: 0.5613 (tptp) cc_final: 0.5311 (tppp) REVERT: J 641 ARG cc_start: 0.6126 (mpt-90) cc_final: 0.4228 (mtm180) REVERT: I 488 PHE cc_start: 0.6869 (p90) cc_final: 0.6635 (p90) REVERT: D 148 LEU cc_start: 0.8632 (mp) cc_final: 0.8004 (tt) REVERT: D 247 ARG cc_start: 0.6929 (mmt90) cc_final: 0.6474 (mmm-85) REVERT: D 368 MET cc_start: 0.8179 (mtp) cc_final: 0.7746 (mtp) REVERT: D 422 ARG cc_start: 0.6686 (pmt-80) cc_final: 0.6330 (ptm160) REVERT: C 137 TYR cc_start: 0.5847 (t80) cc_final: 0.5480 (t80) REVERT: C 306 HIS cc_start: 0.6251 (m90) cc_final: 0.5636 (t70) REVERT: C 389 ILE cc_start: 0.9076 (mt) cc_final: 0.8841 (mm) outliers start: 0 outliers final: 0 residues processed: 462 average time/residue: 0.2341 time to fit residues: 179.7377 Evaluate side-chains 312 residues out of total 4028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 202 optimal weight: 6.9990 chunk 275 optimal weight: 7.9990 chunk 439 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 290 optimal weight: 0.0670 chunk 10 optimal weight: 3.9990 chunk 431 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 273 optimal weight: 6.9990 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 416 GLN K 698 HIS B 416 ASN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN ** I 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 416 GLN I 698 HIS D 416 ASN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.112758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.096945 restraints weight = 154313.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.097641 restraints weight = 210514.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.098616 restraints weight = 165752.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.098679 restraints weight = 122253.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.099642 restraints weight = 105878.720| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37760 Z= 0.129 Angle : 0.585 7.064 51222 Z= 0.308 Chirality : 0.044 0.160 5652 Planarity : 0.004 0.068 6526 Dihedral : 4.503 21.174 5064 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.89 % Favored : 92.06 % Rotamer: Outliers : 0.05 % Allowed : 2.83 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.04 (0.12), residues: 4548 helix: 0.64 (0.13), residues: 1586 sheet: -0.68 (0.18), residues: 812 loop : -1.73 (0.13), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 256 TYR 0.017 0.001 TYR I 439 PHE 0.043 0.002 PHE I 481 TRP 0.029 0.001 TRP K 336 HIS 0.005 0.001 HIS L 612 Details of bonding type rmsd covalent geometry : bond 0.00284 (37744) covalent geometry : angle 0.58431 (51190) SS BOND : bond 0.00263 ( 16) SS BOND : angle 1.06813 ( 32) hydrogen bonds : bond 0.04120 ( 1527) hydrogen bonds : angle 5.17726 ( 4275) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 4028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 421 time to evaluate : 1.501 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: symmetry clash REVERT: L 38 LEU cc_start: 0.7837 (tp) cc_final: 0.7607 (tp) REVERT: L 240 ILE cc_start: 0.6150 (mm) cc_final: 0.5606 (pt) REVERT: L 609 LYS cc_start: 0.5582 (tptp) cc_final: 0.5300 (tppp) REVERT: L 641 ARG cc_start: 0.6173 (mpt-90) cc_final: 0.4247 (mtm180) REVERT: K 104 ARG cc_start: 0.8271 (mtt-85) cc_final: 0.7888 (mtt90) REVERT: K 698 HIS cc_start: 0.5093 (OUTLIER) cc_final: 0.4513 (t70) REVERT: B 247 ARG cc_start: 0.6872 (mmt90) cc_final: 0.6348 (mmm-85) REVERT: B 368 MET cc_start: 0.8010 (mtp) cc_final: 0.7797 (mtp) REVERT: B 422 ARG cc_start: 0.6571 (pmt-80) cc_final: 0.6259 (ptm160) REVERT: A 115 TYR cc_start: 0.5390 (t80) cc_final: 0.5140 (t80) REVERT: A 306 HIS cc_start: 0.6211 (m90) cc_final: 0.5421 (t70) REVERT: A 389 ILE cc_start: 0.9150 (mt) cc_final: 0.8916 (mm) REVERT: J 38 LEU cc_start: 0.7831 (tp) cc_final: 0.7603 (tp) REVERT: J 240 ILE cc_start: 0.6199 (mm) cc_final: 0.5702 (pt) REVERT: J 609 LYS cc_start: 0.5593 (tptp) cc_final: 0.5306 (tppp) REVERT: J 641 ARG cc_start: 0.6161 (mpt-90) cc_final: 0.4228 (mtm180) REVERT: I 698 HIS cc_start: 0.5072 (OUTLIER) cc_final: 0.4486 (t70) REVERT: D 247 ARG cc_start: 0.6866 (mmt90) cc_final: 0.6344 (mmm-85) REVERT: D 422 ARG cc_start: 0.6554 (pmt-80) cc_final: 0.6258 (ptm160) REVERT: C 115 TYR cc_start: 0.5388 (t80) cc_final: 0.5127 (t80) REVERT: C 306 HIS cc_start: 0.6185 (m90) cc_final: 0.5419 (t70) REVERT: C 389 ILE cc_start: 0.9152 (mt) cc_final: 0.8913 (mm) outliers start: 2 outliers final: 0 residues processed: 423 average time/residue: 0.2222 time to fit residues: 156.1031 Evaluate side-chains 303 residues out of total 4028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 301 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 55 optimal weight: 0.9980 chunk 377 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 137 optimal weight: 0.9980 chunk 281 optimal weight: 2.9990 chunk 267 optimal weight: 5.9990 chunk 233 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 200 optimal weight: 0.0970 chunk 115 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 overall best weight: 2.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 209 GLN K 304 HIS K 416 GLN ** K 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 451 GLN ** K 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 209 GLN I 304 HIS ** I 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 416 GLN D 416 ASN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.111947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.096428 restraints weight = 154322.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.094301 restraints weight = 187224.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.093635 restraints weight = 153482.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.093804 restraints weight = 133247.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.093975 restraints weight = 113379.651| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37760 Z= 0.151 Angle : 0.599 7.050 51222 Z= 0.316 Chirality : 0.045 0.196 5652 Planarity : 0.004 0.052 6526 Dihedral : 4.574 19.925 5064 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.07 % Favored : 91.89 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.11 (0.12), residues: 4548 helix: 0.61 (0.13), residues: 1590 sheet: -0.60 (0.18), residues: 800 loop : -1.84 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 296 TYR 0.048 0.002 TYR K 439 PHE 0.033 0.002 PHE K 481 TRP 0.011 0.001 TRP L 244 HIS 0.008 0.001 HIS L 612 Details of bonding type rmsd covalent geometry : bond 0.00341 (37744) covalent geometry : angle 0.59805 (51190) SS BOND : bond 0.00328 ( 16) SS BOND : angle 1.15448 ( 32) hydrogen bonds : bond 0.04087 ( 1527) hydrogen bonds : angle 5.16670 ( 4275) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 4028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 1.595 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: symmetry clash revert: symmetry clash REVERT: L 240 ILE cc_start: 0.6401 (mm) cc_final: 0.5765 (pt) REVERT: L 609 LYS cc_start: 0.5451 (tptp) cc_final: 0.5145 (tptm) REVERT: L 641 ARG cc_start: 0.6227 (mpt-90) cc_final: 0.4389 (mtm180) REVERT: K 104 ARG cc_start: 0.8310 (mtt-85) cc_final: 0.7952 (mtt90) REVERT: K 633 MET cc_start: 0.6565 (tpp) cc_final: 0.6334 (mmt) REVERT: B 148 LEU cc_start: 0.8607 (mp) cc_final: 0.7971 (tt) REVERT: B 183 MET cc_start: 0.6393 (ttt) cc_final: 0.6188 (ttt) REVERT: B 247 ARG cc_start: 0.6717 (mmt90) cc_final: 0.6246 (mmm-85) REVERT: A 115 TYR cc_start: 0.5478 (t80) cc_final: 0.5139 (t80) REVERT: A 137 TYR cc_start: 0.5823 (t80) cc_final: 0.5579 (t80) REVERT: A 306 HIS cc_start: 0.6423 (m90) cc_final: 0.5444 (t70) REVERT: A 389 ILE cc_start: 0.9259 (mt) cc_final: 0.8856 (mm) REVERT: J 38 LEU cc_start: 0.7794 (tp) cc_final: 0.7592 (tp) REVERT: J 240 ILE cc_start: 0.6351 (mm) cc_final: 0.5822 (pt) REVERT: J 609 LYS cc_start: 0.5476 (tptp) cc_final: 0.5170 (tptm) REVERT: J 641 ARG cc_start: 0.6250 (mpt-90) cc_final: 0.4444 (mtp180) REVERT: I 633 MET cc_start: 0.6549 (tpp) cc_final: 0.6338 (mmt) REVERT: D 148 LEU cc_start: 0.8604 (mp) cc_final: 0.7959 (tt) REVERT: D 183 MET cc_start: 0.6381 (ttt) cc_final: 0.6176 (ttt) REVERT: D 247 ARG cc_start: 0.6723 (mmt90) cc_final: 0.6249 (mmm-85) REVERT: C 115 TYR cc_start: 0.5475 (t80) cc_final: 0.5136 (t80) REVERT: C 137 TYR cc_start: 0.5777 (t80) cc_final: 0.5565 (t80) REVERT: C 306 HIS cc_start: 0.6444 (m90) cc_final: 0.5458 (t70) outliers start: 0 outliers final: 0 residues processed: 403 average time/residue: 0.2236 time to fit residues: 150.9200 Evaluate side-chains 283 residues out of total 4028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 257 optimal weight: 20.0000 chunk 85 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 356 optimal weight: 10.0000 chunk 369 optimal weight: 6.9990 chunk 241 optimal weight: 8.9990 chunk 328 optimal weight: 7.9990 chunk 184 optimal weight: 0.9990 chunk 318 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 15 optimal weight: 0.0670 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 304 HIS K 416 GLN ** K 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 698 HIS B 416 ASN ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN I 304 HIS I 416 GLN ** I 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 451 GLN I 698 HIS D 416 ASN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.113263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.097518 restraints weight = 153845.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.097449 restraints weight = 205606.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.098716 restraints weight = 172881.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.098768 restraints weight = 122344.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.100056 restraints weight = 108598.756| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37760 Z= 0.117 Angle : 0.572 6.892 51222 Z= 0.302 Chirality : 0.044 0.184 5652 Planarity : 0.004 0.051 6526 Dihedral : 4.435 19.427 5064 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.23 % Favored : 92.68 % Rotamer: Outliers : 0.05 % Allowed : 2.66 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.12), residues: 4548 helix: 0.71 (0.13), residues: 1578 sheet: -0.47 (0.19), residues: 796 loop : -1.76 (0.13), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 422 TYR 0.042 0.001 TYR K 439 PHE 0.031 0.002 PHE L 781 TRP 0.012 0.001 TRP L 229 HIS 0.006 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00253 (37744) covalent geometry : angle 0.57067 (51190) SS BOND : bond 0.00237 ( 16) SS BOND : angle 1.37213 ( 32) hydrogen bonds : bond 0.03859 ( 1527) hydrogen bonds : angle 5.02388 ( 4275) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 4028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 428 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 240 ILE cc_start: 0.6231 (mm) cc_final: 0.5725 (pt) REVERT: L 529 MET cc_start: 0.6135 (mpp) cc_final: 0.5793 (mpp) REVERT: L 609 LYS cc_start: 0.5520 (tptp) cc_final: 0.5270 (tptm) REVERT: L 641 ARG cc_start: 0.6290 (mpt-90) cc_final: 0.4434 (mtm180) REVERT: L 657 THR cc_start: 0.7824 (p) cc_final: 0.7616 (p) REVERT: K 104 ARG cc_start: 0.8266 (mtt-85) cc_final: 0.7998 (mtt90) REVERT: K 633 MET cc_start: 0.6645 (tpp) cc_final: 0.6377 (mmt) REVERT: B 148 LEU cc_start: 0.8623 (mp) cc_final: 0.8065 (tt) REVERT: B 183 MET cc_start: 0.6542 (ttt) cc_final: 0.6327 (ttt) REVERT: B 247 ARG cc_start: 0.6683 (mmt90) cc_final: 0.6230 (mmm-85) REVERT: B 422 ARG cc_start: 0.6504 (pmt-80) cc_final: 0.6152 (ptm160) REVERT: A 115 TYR cc_start: 0.5480 (t80) cc_final: 0.5162 (t80) REVERT: A 306 HIS cc_start: 0.6117 (m90) cc_final: 0.5265 (t70) REVERT: A 389 ILE cc_start: 0.8969 (mt) cc_final: 0.8720 (mm) REVERT: J 240 ILE cc_start: 0.6159 (mm) cc_final: 0.5674 (pt) REVERT: J 609 LYS cc_start: 0.5523 (tptp) cc_final: 0.5273 (tptm) REVERT: J 641 ARG cc_start: 0.6282 (mpt-90) cc_final: 0.4424 (mtm180) REVERT: J 657 THR cc_start: 0.7839 (p) cc_final: 0.7625 (p) REVERT: I 380 ASP cc_start: 0.6863 (p0) cc_final: 0.6625 (p0) REVERT: I 633 MET cc_start: 0.6646 (tpp) cc_final: 0.6412 (mmt) REVERT: D 148 LEU cc_start: 0.8634 (mp) cc_final: 0.8074 (tt) REVERT: D 183 MET cc_start: 0.6547 (ttt) cc_final: 0.6334 (ttt) REVERT: D 247 ARG cc_start: 0.6683 (mmt90) cc_final: 0.6236 (mmm-85) REVERT: D 422 ARG cc_start: 0.6504 (pmt-80) cc_final: 0.6157 (ptm160) REVERT: C 115 TYR cc_start: 0.5446 (t80) cc_final: 0.5135 (t80) REVERT: C 306 HIS cc_start: 0.6125 (m90) cc_final: 0.5291 (t70) REVERT: C 389 ILE cc_start: 0.8912 (mm) cc_final: 0.8604 (mm) outliers start: 2 outliers final: 2 residues processed: 430 average time/residue: 0.2352 time to fit residues: 168.2514 Evaluate side-chains 311 residues out of total 4028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 309 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 432 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 251 optimal weight: 8.9990 chunk 431 optimal weight: 8.9990 chunk 127 optimal weight: 8.9990 chunk 138 optimal weight: 7.9990 chunk 105 optimal weight: 8.9990 chunk 412 optimal weight: 0.8980 chunk 330 optimal weight: 0.9980 chunk 220 optimal weight: 2.9990 chunk 276 optimal weight: 9.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 416 GLN ** K 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 547 GLN K 606 GLN K 734 HIS B 416 ASN ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 416 GLN I 547 GLN I 606 GLN I 734 HIS D 416 ASN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 GLN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.111162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.095833 restraints weight = 155063.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.094056 restraints weight = 189769.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.093037 restraints weight = 162103.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.093619 restraints weight = 137345.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.093471 restraints weight = 115316.832| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 37760 Z= 0.188 Angle : 0.644 7.310 51222 Z= 0.342 Chirality : 0.046 0.178 5652 Planarity : 0.005 0.068 6526 Dihedral : 4.768 21.175 5064 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.51 % Favored : 91.40 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.12), residues: 4548 helix: 0.55 (0.13), residues: 1584 sheet: -0.66 (0.18), residues: 786 loop : -1.91 (0.12), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 411 TYR 0.036 0.002 TYR K 439 PHE 0.036 0.002 PHE J 785 TRP 0.014 0.002 TRP L 244 HIS 0.008 0.001 HIS J 612 Details of bonding type rmsd covalent geometry : bond 0.00428 (37744) covalent geometry : angle 0.64386 (51190) SS BOND : bond 0.00698 ( 16) SS BOND : angle 1.30802 ( 32) hydrogen bonds : bond 0.04216 ( 1527) hydrogen bonds : angle 5.23490 ( 4275) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 4028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 609 LYS cc_start: 0.5599 (tptp) cc_final: 0.5269 (tptm) REVERT: L 641 ARG cc_start: 0.6239 (mpt-90) cc_final: 0.4491 (mtp180) REVERT: K 308 MET cc_start: 0.6563 (mpp) cc_final: 0.6242 (mpp) REVERT: K 439 TYR cc_start: 0.5098 (m-10) cc_final: 0.4805 (m-80) REVERT: B 148 LEU cc_start: 0.8664 (mp) cc_final: 0.8021 (tt) REVERT: B 247 ARG cc_start: 0.6706 (mmt90) cc_final: 0.6257 (mmm-85) REVERT: J 240 ILE cc_start: 0.6386 (mm) cc_final: 0.5839 (pt) REVERT: J 609 LYS cc_start: 0.5612 (tptp) cc_final: 0.5286 (tptm) REVERT: J 641 ARG cc_start: 0.6244 (mpt-90) cc_final: 0.4510 (mtp180) REVERT: I 439 TYR cc_start: 0.4967 (m-10) cc_final: 0.4710 (m-80) REVERT: D 148 LEU cc_start: 0.8620 (mp) cc_final: 0.8005 (tt) REVERT: D 247 ARG cc_start: 0.6692 (mmt90) cc_final: 0.6236 (mmm-85) REVERT: D 376 MET cc_start: 0.7790 (mtp) cc_final: 0.7572 (mtp) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.2296 time to fit residues: 149.0899 Evaluate side-chains 265 residues out of total 4028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 58 optimal weight: 0.3980 chunk 427 optimal weight: 0.0980 chunk 69 optimal weight: 3.9990 chunk 277 optimal weight: 10.0000 chunk 162 optimal weight: 7.9990 chunk 204 optimal weight: 0.0980 chunk 107 optimal weight: 6.9990 chunk 402 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 376 optimal weight: 0.8980 chunk 227 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 209 GLN K 416 GLN ** K 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 698 HIS B 416 ASN ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 HIS I 209 GLN I 304 HIS ** I 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 416 GLN ** I 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 698 HIS D 416 ASN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 HIS C 425 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.113371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.097509 restraints weight = 152663.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.097647 restraints weight = 202337.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.098810 restraints weight = 170092.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.098827 restraints weight = 120798.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.099312 restraints weight = 108202.817| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 37760 Z= 0.117 Angle : 0.586 7.192 51222 Z= 0.309 Chirality : 0.044 0.173 5652 Planarity : 0.004 0.063 6526 Dihedral : 4.547 19.708 5064 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.79 % Favored : 93.16 % Rotamer: Outliers : 0.05 % Allowed : 1.12 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.00 (0.12), residues: 4548 helix: 0.68 (0.13), residues: 1578 sheet: -0.56 (0.18), residues: 818 loop : -1.76 (0.13), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 147 TYR 0.028 0.001 TYR K 439 PHE 0.030 0.001 PHE L 785 TRP 0.018 0.001 TRP L 423 HIS 0.012 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00250 (37744) covalent geometry : angle 0.58577 (51190) SS BOND : bond 0.00303 ( 16) SS BOND : angle 1.07121 ( 32) hydrogen bonds : bond 0.03784 ( 1527) hydrogen bonds : angle 5.02627 ( 4275) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 4028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 396 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 240 ILE cc_start: 0.6180 (mm) cc_final: 0.5638 (pt) REVERT: L 609 LYS cc_start: 0.5593 (tptp) cc_final: 0.5235 (tptm) REVERT: L 641 ARG cc_start: 0.6135 (mpt-90) cc_final: 0.4390 (mtp180) REVERT: K 698 HIS cc_start: 0.5096 (OUTLIER) cc_final: 0.4595 (t70) REVERT: B 148 LEU cc_start: 0.8673 (mp) cc_final: 0.8129 (tt) REVERT: B 247 ARG cc_start: 0.6789 (mmt90) cc_final: 0.6342 (mmm-85) REVERT: A 202 ASN cc_start: 0.6234 (m110) cc_final: 0.5780 (t0) REVERT: J 240 ILE cc_start: 0.6174 (mm) cc_final: 0.5688 (pt) REVERT: J 546 MET cc_start: 0.4301 (tmm) cc_final: 0.4069 (tmm) REVERT: J 564 LEU cc_start: 0.6688 (tt) cc_final: 0.6047 (mt) REVERT: J 609 LYS cc_start: 0.5598 (tptp) cc_final: 0.5230 (tptm) REVERT: J 641 ARG cc_start: 0.6119 (mpt-90) cc_final: 0.4385 (mtp180) REVERT: I 308 MET cc_start: 0.6763 (mpp) cc_final: 0.6435 (mpp) REVERT: I 698 HIS cc_start: 0.5049 (OUTLIER) cc_final: 0.4536 (t70) REVERT: D 148 LEU cc_start: 0.8656 (mp) cc_final: 0.8101 (tt) REVERT: D 247 ARG cc_start: 0.6789 (mmt90) cc_final: 0.6349 (mmm-85) REVERT: C 202 ASN cc_start: 0.6340 (m110) cc_final: 0.5804 (t0) outliers start: 2 outliers final: 0 residues processed: 398 average time/residue: 0.2272 time to fit residues: 151.6905 Evaluate side-chains 292 residues out of total 4028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 290 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 99 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 421 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 345 optimal weight: 10.0000 chunk 309 optimal weight: 8.9990 chunk 348 optimal weight: 0.5980 chunk 425 optimal weight: 0.0670 chunk 39 optimal weight: 20.0000 chunk 158 optimal weight: 20.0000 overall best weight: 3.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 416 GLN ** K 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 762 HIS K 772 HIS B 416 ASN ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 416 GLN ** I 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.111144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.095996 restraints weight = 153959.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.094104 restraints weight = 191651.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.092798 restraints weight = 169465.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.093114 restraints weight = 157864.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.093246 restraints weight = 120419.929| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 37760 Z= 0.194 Angle : 0.658 8.661 51222 Z= 0.348 Chirality : 0.046 0.194 5652 Planarity : 0.005 0.055 6526 Dihedral : 4.823 22.056 5064 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.73 % Favored : 91.23 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.23 (0.12), residues: 4548 helix: 0.53 (0.13), residues: 1582 sheet: -0.66 (0.18), residues: 798 loop : -1.93 (0.12), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 142 TYR 0.040 0.002 TYR K 439 PHE 0.037 0.002 PHE A 194 TRP 0.019 0.002 TRP I 583 HIS 0.007 0.001 HIS J 612 Details of bonding type rmsd covalent geometry : bond 0.00442 (37744) covalent geometry : angle 0.65780 (51190) SS BOND : bond 0.00675 ( 16) SS BOND : angle 1.27489 ( 32) hydrogen bonds : bond 0.04229 ( 1527) hydrogen bonds : angle 5.24774 ( 4275) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 4028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 609 LYS cc_start: 0.5582 (tptp) cc_final: 0.5202 (tptm) REVERT: L 641 ARG cc_start: 0.6262 (mpt-90) cc_final: 0.4513 (mtp-110) REVERT: K 308 MET cc_start: 0.6562 (mpp) cc_final: 0.6184 (mpp) REVERT: K 633 MET cc_start: 0.6665 (mmt) cc_final: 0.6392 (mmt) REVERT: B 148 LEU cc_start: 0.8704 (mp) cc_final: 0.8158 (tt) REVERT: B 247 ARG cc_start: 0.6844 (mmt90) cc_final: 0.6457 (mmm-85) REVERT: A 317 LEU cc_start: 0.8873 (mm) cc_final: 0.8511 (mm) REVERT: J 240 ILE cc_start: 0.6499 (mm) cc_final: 0.5944 (pt) REVERT: J 546 MET cc_start: 0.4158 (tmm) cc_final: 0.3862 (tmm) REVERT: J 564 LEU cc_start: 0.6942 (tt) cc_final: 0.6343 (tp) REVERT: J 609 LYS cc_start: 0.5588 (tptp) cc_final: 0.5213 (tptm) REVERT: J 641 ARG cc_start: 0.6272 (mpt-90) cc_final: 0.4492 (mtp-110) REVERT: I 633 MET cc_start: 0.6614 (mmt) cc_final: 0.6266 (mmt) REVERT: D 148 LEU cc_start: 0.8706 (mp) cc_final: 0.8160 (tt) REVERT: D 247 ARG cc_start: 0.6833 (mmt90) cc_final: 0.6449 (mmm-85) REVERT: C 317 LEU cc_start: 0.8851 (mm) cc_final: 0.8497 (mm) outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.2279 time to fit residues: 141.9795 Evaluate side-chains 270 residues out of total 4028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 350 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 346 optimal weight: 9.9990 chunk 95 optimal weight: 0.3980 chunk 298 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 377 optimal weight: 0.8980 chunk 236 optimal weight: 0.5980 chunk 344 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 209 GLN K 416 GLN ** K 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 698 HIS B 416 ASN ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 209 GLN I 304 HIS ** I 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 416 GLN ** I 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 698 HIS D 416 ASN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.113275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.098002 restraints weight = 153693.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.096233 restraints weight = 181329.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.095171 restraints weight = 151187.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.095543 restraints weight = 134601.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.095673 restraints weight = 107901.271| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37760 Z= 0.120 Angle : 0.612 13.678 51222 Z= 0.317 Chirality : 0.044 0.173 5652 Planarity : 0.004 0.055 6526 Dihedral : 4.599 21.090 5064 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.04 % Favored : 92.92 % Rotamer: Outliers : 0.05 % Allowed : 0.47 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.04 (0.12), residues: 4548 helix: 0.67 (0.13), residues: 1576 sheet: -0.62 (0.18), residues: 806 loop : -1.77 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 382 TYR 0.030 0.001 TYR K 439 PHE 0.031 0.001 PHE J 785 TRP 0.012 0.001 TRP K 88 HIS 0.009 0.001 HIS I 304 Details of bonding type rmsd covalent geometry : bond 0.00260 (37744) covalent geometry : angle 0.61112 (51190) SS BOND : bond 0.00248 ( 16) SS BOND : angle 1.09335 ( 32) hydrogen bonds : bond 0.03835 ( 1527) hydrogen bonds : angle 5.02979 ( 4275) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 4028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 386 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 240 ILE cc_start: 0.6400 (mm) cc_final: 0.5810 (pt) REVERT: L 609 LYS cc_start: 0.5584 (tptp) cc_final: 0.5241 (tptm) REVERT: L 641 ARG cc_start: 0.6299 (mpt-90) cc_final: 0.4581 (mtp-110) REVERT: K 308 MET cc_start: 0.6708 (mpp) cc_final: 0.6442 (mpp) REVERT: K 698 HIS cc_start: 0.5359 (OUTLIER) cc_final: 0.4987 (t70) REVERT: B 148 LEU cc_start: 0.8610 (mp) cc_final: 0.8064 (tt) REVERT: B 247 ARG cc_start: 0.6703 (mmt90) cc_final: 0.6376 (mmm-85) REVERT: J 240 ILE cc_start: 0.6441 (mm) cc_final: 0.5883 (pt) REVERT: J 546 MET cc_start: 0.4338 (tmm) cc_final: 0.4050 (tmm) REVERT: J 564 LEU cc_start: 0.6923 (tt) cc_final: 0.6355 (tp) REVERT: J 609 LYS cc_start: 0.5581 (tptp) cc_final: 0.5232 (tptm) REVERT: J 641 ARG cc_start: 0.6287 (mpt-90) cc_final: 0.4573 (mtp-110) REVERT: I 308 MET cc_start: 0.6764 (mpp) cc_final: 0.6438 (mpp) REVERT: I 698 HIS cc_start: 0.5346 (OUTLIER) cc_final: 0.4974 (t70) REVERT: D 148 LEU cc_start: 0.8590 (mp) cc_final: 0.8049 (tt) REVERT: D 247 ARG cc_start: 0.6698 (mmt90) cc_final: 0.6366 (mmm-85) outliers start: 2 outliers final: 0 residues processed: 388 average time/residue: 0.2264 time to fit residues: 147.6149 Evaluate side-chains 280 residues out of total 4028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 278 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 452 random chunks: chunk 450 optimal weight: 0.9990 chunk 258 optimal weight: 0.0470 chunk 395 optimal weight: 0.8980 chunk 255 optimal weight: 4.9990 chunk 167 optimal weight: 0.0670 chunk 441 optimal weight: 2.9990 chunk 352 optimal weight: 8.9990 chunk 238 optimal weight: 6.9990 chunk 262 optimal weight: 0.7980 chunk 217 optimal weight: 3.9990 chunk 386 optimal weight: 3.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 209 GLN K 239 HIS K 416 GLN ** K 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN ** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 209 GLN ** I 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 416 GLN ** I 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.113845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.098273 restraints weight = 152701.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.098592 restraints weight = 208650.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.099687 restraints weight = 171441.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.099652 restraints weight = 130231.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.100264 restraints weight = 111261.846| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37760 Z= 0.117 Angle : 0.603 12.725 51222 Z= 0.314 Chirality : 0.044 0.197 5652 Planarity : 0.004 0.053 6526 Dihedral : 4.481 21.666 5064 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.85 % Favored : 92.11 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.12), residues: 4548 helix: 0.68 (0.13), residues: 1578 sheet: -0.57 (0.18), residues: 806 loop : -1.72 (0.13), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 97 TYR 0.027 0.001 TYR I 439 PHE 0.039 0.001 PHE C 194 TRP 0.019 0.001 TRP L 423 HIS 0.006 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00250 (37744) covalent geometry : angle 0.60264 (51190) SS BOND : bond 0.00207 ( 16) SS BOND : angle 1.29757 ( 32) hydrogen bonds : bond 0.03729 ( 1527) hydrogen bonds : angle 4.97315 ( 4275) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5831.90 seconds wall clock time: 102 minutes 34.62 seconds (6154.62 seconds total)