Starting phenix.real_space_refine on Tue Sep 15 06:39:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6cvm_7770/09_2026/6cvm_7770.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cvm_7770/09_2026/6cvm_7770.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6cvm_7770/09_2026/6cvm_7770.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cvm_7770/09_2026/6cvm_7770.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6cvm_7770/09_2026/6cvm_7770.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6cvm_7770/09_2026/6cvm_7770.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6cvm_7770/09_2026/6cvm_7770.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cvm_7770/09_2026/6cvm_7770.map" } resolution = 1.9 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= -0.008 sd= 0.159 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mg 8 5.21 5 S 160 5.16 5 Na 8 4.78 5 C 20792 2.51 5 N 5800 2.21 5 O 10294 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 156 residue(s): 0.24s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 37062 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1021, 8193 Classifications: {'peptide': 1021} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 955} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 24 Unusual residues: {' MG': 2, ' NA': 2, 'PTQ': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1047, 1047 Classifications: {'water': 1047} Link IDs: {None: 1046} Chain: "B" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 1048 Classifications: {'water': 1048} Link IDs: {None: 1047} Chain: "C" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 1050 Classifications: {'water': 1050} Link IDs: {None: 1049} Chain: "D" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1049, 1049 Classifications: {'water': 1049} Link IDs: {None: 1048} Restraints were copied for chains: B, C, D Time building chain proxies: 13.26, per 1000 atoms: 0.36 Number of scatterers: 37062 At special positions: 0 Unit cell: (191.737, 150.969, 100.009, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 160 16.00 Mg 8 11.99 Na 8 11.00 O 10294 8.00 N 5800 7.00 C 20792 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.03 Conformation dependent library (CDL) restraints added in 1.5 seconds 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7600 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 56 sheets defined 17.7% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 6 through 11 Processing helix chain 'A' and resid 14 through 18 removed outlier: 3.540A pdb=" N ASN A 18 " --> pdb=" O ASP A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 44 Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 89 through 94 removed outlier: 3.555A pdb=" N GLY A 94 " --> pdb=" O GLN A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 136 removed outlier: 4.191A pdb=" N GLU A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 198 Processing helix chain 'A' and resid 368 through 381 Processing helix chain 'A' and resid 395 through 406 removed outlier: 4.177A pdb=" N TYR A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 448 removed outlier: 3.604A pdb=" N ARG A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.687A pdb=" N ASP A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 525 removed outlier: 3.597A pdb=" N LEU A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER A 525 " --> pdb=" O LYS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.913A pdb=" N TYR A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 603 removed outlier: 3.995A pdb=" N CYS A 602 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 624 removed outlier: 3.930A pdb=" N GLU A 619 " --> pdb=" O PRO A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 805 through 813 Processing helix chain 'A' and resid 923 through 926 removed outlier: 3.538A pdb=" N TYR A 926 " --> pdb=" O SER A 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 923 through 926' Processing helix chain 'A' and resid 963 through 970 Processing helix chain 'A' and resid 972 through 976 Processing helix chain 'A' and resid 1004 through 1008 Processing helix chain 'B' and resid 6 through 11 Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.540A pdb=" N ASN B 18 " --> pdb=" O ASP B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 44 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 89 through 94 removed outlier: 3.555A pdb=" N GLY B 94 " --> pdb=" O GLN B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 136 removed outlier: 4.191A pdb=" N GLU B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 198 Processing helix chain 'B' and resid 368 through 381 Processing helix chain 'B' and resid 395 through 406 removed outlier: 4.177A pdb=" N TYR B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 432 through 448 removed outlier: 3.604A pdb=" N ARG B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 479 removed outlier: 3.687A pdb=" N ASP B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 525 removed outlier: 3.597A pdb=" N LEU B 524 " --> pdb=" O ILE B 520 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER B 525 " --> pdb=" O LYS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 559 removed outlier: 3.913A pdb=" N TYR B 552 " --> pdb=" O GLY B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 603 removed outlier: 3.994A pdb=" N CYS B 602 " --> pdb=" O ARG B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 624 removed outlier: 3.930A pdb=" N GLU B 619 " --> pdb=" O PRO B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 794 Processing helix chain 'B' and resid 805 through 813 Processing helix chain 'B' and resid 923 through 926 removed outlier: 3.538A pdb=" N TYR B 926 " --> pdb=" O SER B 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 923 through 926' Processing helix chain 'B' and resid 963 through 970 Processing helix chain 'B' and resid 972 through 976 Processing helix chain 'B' and resid 1004 through 1008 Processing helix chain 'C' and resid 6 through 11 Processing helix chain 'C' and resid 14 through 18 removed outlier: 3.540A pdb=" N ASN C 18 " --> pdb=" O ASP C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 44 Processing helix chain 'C' and resid 65 through 69 Processing helix chain 'C' and resid 70 through 75 Processing helix chain 'C' and resid 89 through 94 removed outlier: 3.555A pdb=" N GLY C 94 " --> pdb=" O GLN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 136 removed outlier: 4.191A pdb=" N GLU C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 198 Processing helix chain 'C' and resid 368 through 381 Processing helix chain 'C' and resid 395 through 406 removed outlier: 4.177A pdb=" N TYR C 399 " --> pdb=" O HIS C 395 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 431 No H-bonds generated for 'chain 'C' and resid 429 through 431' Processing helix chain 'C' and resid 432 through 448 removed outlier: 3.604A pdb=" N ARG C 439 " --> pdb=" O ALA C 435 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 479 removed outlier: 3.687A pdb=" N ASP C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 525 removed outlier: 3.597A pdb=" N LEU C 524 " --> pdb=" O ILE C 520 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER C 525 " --> pdb=" O LYS C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 559 removed outlier: 3.913A pdb=" N TYR C 552 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 603 removed outlier: 3.994A pdb=" N CYS C 602 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 624 removed outlier: 3.929A pdb=" N GLU C 619 " --> pdb=" O PRO C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 794 Processing helix chain 'C' and resid 805 through 813 Processing helix chain 'C' and resid 923 through 926 removed outlier: 3.538A pdb=" N TYR C 926 " --> pdb=" O SER C 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 923 through 926' Processing helix chain 'C' and resid 963 through 970 Processing helix chain 'C' and resid 972 through 976 Processing helix chain 'C' and resid 1004 through 1008 Processing helix chain 'D' and resid 6 through 11 Processing helix chain 'D' and resid 14 through 18 removed outlier: 3.540A pdb=" N ASN D 18 " --> pdb=" O ASP D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 44 Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 70 through 75 Processing helix chain 'D' and resid 89 through 94 removed outlier: 3.554A pdb=" N GLY D 94 " --> pdb=" O GLN D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 136 removed outlier: 4.191A pdb=" N GLU D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 198 Processing helix chain 'D' and resid 368 through 381 Processing helix chain 'D' and resid 395 through 406 removed outlier: 4.177A pdb=" N TYR D 399 " --> pdb=" O HIS D 395 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR D 400 " --> pdb=" O PRO D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 431 No H-bonds generated for 'chain 'D' and resid 429 through 431' Processing helix chain 'D' and resid 432 through 448 removed outlier: 3.604A pdb=" N ARG D 439 " --> pdb=" O ALA D 435 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET D 443 " --> pdb=" O ARG D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 479 removed outlier: 3.686A pdb=" N ASP D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 525 removed outlier: 3.597A pdb=" N LEU D 524 " --> pdb=" O ILE D 520 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER D 525 " --> pdb=" O LYS D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.913A pdb=" N TYR D 552 " --> pdb=" O GLY D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 603 removed outlier: 3.996A pdb=" N CYS D 602 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 624 removed outlier: 3.930A pdb=" N GLU D 619 " --> pdb=" O PRO D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 794 Processing helix chain 'D' and resid 805 through 813 Processing helix chain 'D' and resid 923 through 926 removed outlier: 3.538A pdb=" N TYR D 926 " --> pdb=" O SER D 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 923 through 926' Processing helix chain 'D' and resid 963 through 970 Processing helix chain 'D' and resid 972 through 976 Processing helix chain 'D' and resid 1004 through 1008 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 removed outlier: 6.720A pdb=" N LEU A 152 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR A 161 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE A 150 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY A 180 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N THR A 126 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N GLU A 57 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.069A pdb=" N THR A 101 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET A 202 " --> pdb=" O THR A 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA5, first strand: chain 'A' and resid 221 through 231 removed outlier: 5.441A pdb=" N ILE A 222 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N CYS A 247 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 273 removed outlier: 5.594A pdb=" N GLN A 266 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLN A 262 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR A 317 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU A 322 " --> pdb=" O THR A 317 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 335 through 338 Processing sheet with id=AA8, first strand: chain 'A' and resid 484 through 485 removed outlier: 8.043A pdb=" N GLN A 485 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N TRP A 456 " --> pdb=" O GLN A 485 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL A 409 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N SER A 457 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASP A 411 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU A 412 " --> pdb=" O CYS A 389 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ARG A 352 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ARG A 388 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL A 354 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU A 533 " --> pdb=" O GLY A 564 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N PHE A 566 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU A 535 " --> pdb=" O PHE A 566 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 575 through 578 Processing sheet with id=AB1, first strand: chain 'A' and resid 627 through 632 Processing sheet with id=AB2, first strand: chain 'A' and resid 661 through 669 removed outlier: 6.024A pdb=" N LEU A 658 " --> pdb=" O PRO A 662 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLY A 692 " --> pdb=" O GLU A 724 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLU A 724 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU A 694 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A 716 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLN A 702 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE A 714 " --> pdb=" O GLN A 702 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 739 through 742 removed outlier: 6.235A pdb=" N ASN A 759 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU A 765 " --> pdb=" O ASN A 759 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 776 through 783 removed outlier: 6.387A pdb=" N GLN A 887 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ASN A 885 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG A 781 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY A 883 " --> pdb=" O ARG A 781 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLN A 783 " --> pdb=" O ARG A 881 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ARG A 881 " --> pdb=" O GLN A 783 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 11.883A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP A 954 " --> pdb=" O GLN A1017 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLN A1017 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N GLN A 956 " --> pdb=" O HIS A1015 " (cutoff:3.500A) removed outlier: 13.399A pdb=" N HIS A1015 " --> pdb=" O GLN A 956 " (cutoff:3.500A) removed outlier: 20.403A pdb=" N ASN A 958 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 23.382A pdb=" N ARG A1013 " --> pdb=" O ASN A 958 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N THR A 848 " --> pdb=" O HIS A 844 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N HIS A 844 " --> pdb=" O THR A 848 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA A 833 " --> pdb=" O THR A 829 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N THR A 829 " --> pdb=" O ALA A 833 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU A 835 " --> pdb=" O ALA A 827 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA A 827 " --> pdb=" O LEU A 835 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR A 837 " --> pdb=" O CYS A 825 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N CYS A 825 " --> pdb=" O THR A 837 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA A 839 " --> pdb=" O LEU A 823 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A 819 " --> pdb=" O GLN A 843 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 776 through 783 removed outlier: 6.387A pdb=" N GLN A 887 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ASN A 885 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG A 781 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY A 883 " --> pdb=" O ARG A 781 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLN A 783 " --> pdb=" O ARG A 881 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ARG A 881 " --> pdb=" O GLN A 783 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 11.883A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ARG A 942 " --> pdb=" O GLY A 953 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N PHE A 955 " --> pdb=" O GLY A 940 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY A 940 " --> pdb=" O PHE A 955 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR A 941 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LEU A 900 " --> pdb=" O THR A 941 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 23 through 24 removed outlier: 6.720A pdb=" N LEU B 152 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR B 161 " --> pdb=" O PHE B 150 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE B 150 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY B 180 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N THR B 126 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N GLU B 57 " --> pdb=" O THR B 126 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AB8, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.069A pdb=" N THR B 101 " --> pdb=" O MET B 202 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET B 202 " --> pdb=" O THR B 101 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AC1, first strand: chain 'B' and resid 221 through 231 removed outlier: 5.441A pdb=" N ILE B 222 " --> pdb=" O CYS B 247 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N CYS B 247 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 265 through 273 removed outlier: 5.595A pdb=" N GLN B 266 " --> pdb=" O GLN B 262 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLN B 262 " --> pdb=" O GLN B 266 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N THR B 317 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU B 322 " --> pdb=" O THR B 317 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 335 through 338 Processing sheet with id=AC4, first strand: chain 'B' and resid 484 through 485 removed outlier: 8.043A pdb=" N GLN B 485 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TRP B 456 " --> pdb=" O GLN B 485 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL B 409 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N SER B 457 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASP B 411 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU B 412 " --> pdb=" O CYS B 389 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ARG B 352 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ARG B 388 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 354 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU B 533 " --> pdb=" O GLY B 564 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N PHE B 566 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU B 535 " --> pdb=" O PHE B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 575 through 578 Processing sheet with id=AC6, first strand: chain 'B' and resid 627 through 632 Processing sheet with id=AC7, first strand: chain 'B' and resid 661 through 669 removed outlier: 6.024A pdb=" N LEU B 658 " --> pdb=" O PRO B 662 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY B 692 " --> pdb=" O GLU B 724 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLU B 724 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU B 694 " --> pdb=" O LEU B 722 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA B 716 " --> pdb=" O VAL B 700 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLN B 702 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE B 714 " --> pdb=" O GLN B 702 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 739 through 742 removed outlier: 6.235A pdb=" N ASN B 759 " --> pdb=" O LEU B 765 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU B 765 " --> pdb=" O ASN B 759 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 776 through 783 removed outlier: 6.387A pdb=" N GLN B 887 " --> pdb=" O LEU B 777 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ASN B 885 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG B 781 " --> pdb=" O GLY B 883 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLY B 883 " --> pdb=" O ARG B 781 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLN B 783 " --> pdb=" O ARG B 881 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ARG B 881 " --> pdb=" O GLN B 783 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 11.883A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP B 954 " --> pdb=" O GLN B1017 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLN B1017 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N GLN B 956 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 13.400A pdb=" N HIS B1015 " --> pdb=" O GLN B 956 " (cutoff:3.500A) removed outlier: 20.404A pdb=" N ASN B 958 " --> pdb=" O ARG B1013 " (cutoff:3.500A) removed outlier: 23.383A pdb=" N ARG B1013 " --> pdb=" O ASN B 958 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N THR B 848 " --> pdb=" O HIS B 844 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N HIS B 844 " --> pdb=" O THR B 848 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA B 833 " --> pdb=" O THR B 829 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N THR B 829 " --> pdb=" O ALA B 833 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU B 835 " --> pdb=" O ALA B 827 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA B 827 " --> pdb=" O LEU B 835 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR B 837 " --> pdb=" O CYS B 825 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N CYS B 825 " --> pdb=" O THR B 837 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA B 839 " --> pdb=" O LEU B 823 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU B 819 " --> pdb=" O GLN B 843 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 776 through 783 removed outlier: 6.387A pdb=" N GLN B 887 " --> pdb=" O LEU B 777 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ASN B 885 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG B 781 " --> pdb=" O GLY B 883 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLY B 883 " --> pdb=" O ARG B 781 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLN B 783 " --> pdb=" O ARG B 881 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ARG B 881 " --> pdb=" O GLN B 783 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 11.883A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG B 942 " --> pdb=" O GLY B 953 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N PHE B 955 " --> pdb=" O GLY B 940 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY B 940 " --> pdb=" O PHE B 955 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N THR B 941 " --> pdb=" O LEU B 900 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LEU B 900 " --> pdb=" O THR B 941 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 23 through 24 removed outlier: 6.719A pdb=" N LEU C 152 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR C 161 " --> pdb=" O PHE C 150 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE C 150 " --> pdb=" O TYR C 161 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY C 180 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N THR C 126 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N GLU C 57 " --> pdb=" O THR C 126 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 51 through 53 Processing sheet with id=AD4, first strand: chain 'C' and resid 99 through 101 removed outlier: 4.069A pdb=" N THR C 101 " --> pdb=" O MET C 202 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET C 202 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 146 through 147 Processing sheet with id=AD6, first strand: chain 'C' and resid 221 through 231 removed outlier: 5.441A pdb=" N ILE C 222 " --> pdb=" O CYS C 247 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N CYS C 247 " --> pdb=" O ILE C 222 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 265 through 273 removed outlier: 5.594A pdb=" N GLN C 266 " --> pdb=" O GLN C 262 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLN C 262 " --> pdb=" O GLN C 266 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR C 317 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU C 322 " --> pdb=" O THR C 317 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 335 through 338 Processing sheet with id=AD9, first strand: chain 'C' and resid 484 through 485 removed outlier: 8.043A pdb=" N GLN C 485 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N TRP C 456 " --> pdb=" O GLN C 485 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL C 409 " --> pdb=" O ILE C 455 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N SER C 457 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASP C 411 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU C 412 " --> pdb=" O CYS C 389 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ARG C 352 " --> pdb=" O ALA C 386 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ARG C 388 " --> pdb=" O ARG C 352 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL C 354 " --> pdb=" O ARG C 388 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU C 533 " --> pdb=" O GLY C 564 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N PHE C 566 " --> pdb=" O LEU C 533 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU C 535 " --> pdb=" O PHE C 566 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 575 through 578 Processing sheet with id=AE2, first strand: chain 'C' and resid 627 through 632 Processing sheet with id=AE3, first strand: chain 'C' and resid 661 through 669 removed outlier: 6.024A pdb=" N LEU C 658 " --> pdb=" O PRO C 662 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY C 692 " --> pdb=" O GLU C 724 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLU C 724 " --> pdb=" O GLY C 692 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU C 694 " --> pdb=" O LEU C 722 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA C 716 " --> pdb=" O VAL C 700 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLN C 702 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE C 714 " --> pdb=" O GLN C 702 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 739 through 742 removed outlier: 6.235A pdb=" N ASN C 759 " --> pdb=" O LEU C 765 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU C 765 " --> pdb=" O ASN C 759 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 776 through 783 removed outlier: 6.387A pdb=" N GLN C 887 " --> pdb=" O LEU C 777 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN C 885 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG C 781 " --> pdb=" O GLY C 883 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY C 883 " --> pdb=" O ARG C 781 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLN C 783 " --> pdb=" O ARG C 881 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ARG C 881 " --> pdb=" O GLN C 783 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 11.883A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP C 954 " --> pdb=" O GLN C1017 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLN C1017 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 10.406A pdb=" N GLN C 956 " --> pdb=" O HIS C1015 " (cutoff:3.500A) removed outlier: 13.400A pdb=" N HIS C1015 " --> pdb=" O GLN C 956 " (cutoff:3.500A) removed outlier: 20.404A pdb=" N ASN C 958 " --> pdb=" O ARG C1013 " (cutoff:3.500A) removed outlier: 23.384A pdb=" N ARG C1013 " --> pdb=" O ASN C 958 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N THR C 848 " --> pdb=" O HIS C 844 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N HIS C 844 " --> pdb=" O THR C 848 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA C 833 " --> pdb=" O THR C 829 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N THR C 829 " --> pdb=" O ALA C 833 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU C 835 " --> pdb=" O ALA C 827 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA C 827 " --> pdb=" O LEU C 835 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR C 837 " --> pdb=" O CYS C 825 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N CYS C 825 " --> pdb=" O THR C 837 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA C 839 " --> pdb=" O LEU C 823 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C 819 " --> pdb=" O GLN C 843 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 776 through 783 removed outlier: 6.387A pdb=" N GLN C 887 " --> pdb=" O LEU C 777 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN C 885 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG C 781 " --> pdb=" O GLY C 883 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY C 883 " --> pdb=" O ARG C 781 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLN C 783 " --> pdb=" O ARG C 881 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ARG C 881 " --> pdb=" O GLN C 783 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 11.883A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG C 942 " --> pdb=" O GLY C 953 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N PHE C 955 " --> pdb=" O GLY C 940 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY C 940 " --> pdb=" O PHE C 955 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR C 941 " --> pdb=" O LEU C 900 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU C 900 " --> pdb=" O THR C 941 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 23 through 24 removed outlier: 6.720A pdb=" N LEU D 152 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR D 161 " --> pdb=" O PHE D 150 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE D 150 " --> pdb=" O TYR D 161 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY D 180 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N THR D 126 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N GLU D 57 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AE9, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.069A pdb=" N THR D 101 " --> pdb=" O MET D 202 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET D 202 " --> pdb=" O THR D 101 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 146 through 147 Processing sheet with id=AF2, first strand: chain 'D' and resid 221 through 231 removed outlier: 5.441A pdb=" N ILE D 222 " --> pdb=" O CYS D 247 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N CYS D 247 " --> pdb=" O ILE D 222 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 265 through 273 removed outlier: 5.594A pdb=" N GLN D 266 " --> pdb=" O GLN D 262 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLN D 262 " --> pdb=" O GLN D 266 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR D 317 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU D 322 " --> pdb=" O THR D 317 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 335 through 338 Processing sheet with id=AF5, first strand: chain 'D' and resid 484 through 485 removed outlier: 8.043A pdb=" N GLN D 485 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N TRP D 456 " --> pdb=" O GLN D 485 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL D 409 " --> pdb=" O ILE D 455 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N SER D 457 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASP D 411 " --> pdb=" O SER D 457 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU D 412 " --> pdb=" O CYS D 389 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ARG D 352 " --> pdb=" O ALA D 386 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ARG D 388 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL D 354 " --> pdb=" O ARG D 388 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU D 533 " --> pdb=" O GLY D 564 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N PHE D 566 " --> pdb=" O LEU D 533 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU D 535 " --> pdb=" O PHE D 566 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 575 through 578 Processing sheet with id=AF7, first strand: chain 'D' and resid 627 through 632 Processing sheet with id=AF8, first strand: chain 'D' and resid 661 through 669 removed outlier: 6.024A pdb=" N LEU D 658 " --> pdb=" O PRO D 662 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY D 692 " --> pdb=" O GLU D 724 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLU D 724 " --> pdb=" O GLY D 692 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU D 694 " --> pdb=" O LEU D 722 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA D 716 " --> pdb=" O VAL D 700 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLN D 702 " --> pdb=" O ILE D 714 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE D 714 " --> pdb=" O GLN D 702 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 739 through 742 removed outlier: 6.235A pdb=" N ASN D 759 " --> pdb=" O LEU D 765 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU D 765 " --> pdb=" O ASN D 759 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 776 through 783 removed outlier: 6.389A pdb=" N GLN D 887 " --> pdb=" O LEU D 777 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN D 885 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG D 781 " --> pdb=" O GLY D 883 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY D 883 " --> pdb=" O ARG D 781 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLN D 783 " --> pdb=" O ARG D 881 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ARG D 881 " --> pdb=" O GLN D 783 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 11.883A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP D 954 " --> pdb=" O GLN D1017 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLN D1017 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 10.408A pdb=" N GLN D 956 " --> pdb=" O HIS D1015 " (cutoff:3.500A) removed outlier: 13.401A pdb=" N HIS D1015 " --> pdb=" O GLN D 956 " (cutoff:3.500A) removed outlier: 20.404A pdb=" N ASN D 958 " --> pdb=" O ARG D1013 " (cutoff:3.500A) removed outlier: 23.383A pdb=" N ARG D1013 " --> pdb=" O ASN D 958 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N THR D 848 " --> pdb=" O HIS D 844 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N HIS D 844 " --> pdb=" O THR D 848 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA D 833 " --> pdb=" O THR D 829 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N THR D 829 " --> pdb=" O ALA D 833 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU D 835 " --> pdb=" O ALA D 827 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA D 827 " --> pdb=" O LEU D 835 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR D 837 " --> pdb=" O CYS D 825 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N CYS D 825 " --> pdb=" O THR D 837 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA D 839 " --> pdb=" O LEU D 823 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU D 819 " --> pdb=" O GLN D 843 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 776 through 783 removed outlier: 6.389A pdb=" N GLN D 887 " --> pdb=" O LEU D 777 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN D 885 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ARG D 781 " --> pdb=" O GLY D 883 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLY D 883 " --> pdb=" O ARG D 781 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLN D 783 " --> pdb=" O ARG D 881 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ARG D 881 " --> pdb=" O GLN D 783 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 11.883A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG D 942 " --> pdb=" O GLY D 953 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N PHE D 955 " --> pdb=" O GLY D 940 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY D 940 " --> pdb=" O PHE D 955 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR D 941 " --> pdb=" O LEU D 900 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LEU D 900 " --> pdb=" O THR D 941 " (cutoff:3.500A) 1264 hydrogen bonds defined for protein. 3276 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: 12.80 Time building geometry restraints manager: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 5576 1.31 - 1.44: 9779 1.44 - 1.56: 18213 1.56 - 1.69: 0 1.69 - 1.81: 256 Bond restraints: 33824 Sorted by residual: bond pdb=" C13 PTQ B2001 " pdb=" C14 PTQ B2001 " ideal model delta sigma weight residual 1.389 1.514 -0.125 2.00e-02 2.50e+03 3.93e+01 bond pdb=" C13 PTQ C2001 " pdb=" C14 PTQ C2001 " ideal model delta sigma weight residual 1.389 1.514 -0.125 2.00e-02 2.50e+03 3.93e+01 bond pdb=" C13 PTQ A2001 " pdb=" C14 PTQ A2001 " ideal model delta sigma weight residual 1.389 1.514 -0.125 2.00e-02 2.50e+03 3.93e+01 bond pdb=" C13 PTQ D2001 " pdb=" C14 PTQ D2001 " ideal model delta sigma weight residual 1.389 1.514 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C11 PTQ D2001 " pdb=" C12 PTQ D2001 " ideal model delta sigma weight residual 1.389 1.510 -0.121 2.00e-02 2.50e+03 3.67e+01 ... (remaining 33819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 44340 2.10 - 4.21: 1570 4.21 - 6.31: 194 6.31 - 8.42: 36 8.42 - 10.52: 16 Bond angle restraints: 46156 Sorted by residual: angle pdb=" N VAL A 334 " pdb=" CA VAL A 334 " pdb=" CB VAL A 334 " ideal model delta sigma weight residual 111.52 118.22 -6.70 1.46e+00 4.69e-01 2.10e+01 angle pdb=" C PRO A 513 " pdb=" N ALA A 514 " pdb=" CA ALA A 514 " ideal model delta sigma weight residual 121.54 130.27 -8.73 1.91e+00 2.74e-01 2.09e+01 angle pdb=" C PRO B 513 " pdb=" N ALA B 514 " pdb=" CA ALA B 514 " ideal model delta sigma weight residual 121.54 130.27 -8.73 1.91e+00 2.74e-01 2.09e+01 angle pdb=" N VAL D 334 " pdb=" CA VAL D 334 " pdb=" CB VAL D 334 " ideal model delta sigma weight residual 111.52 118.19 -6.67 1.46e+00 4.69e-01 2.09e+01 angle pdb=" N VAL B 334 " pdb=" CA VAL B 334 " pdb=" CB VAL B 334 " ideal model delta sigma weight residual 111.52 118.19 -6.67 1.46e+00 4.69e-01 2.09e+01 ... (remaining 46151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.58: 18671 15.58 - 31.15: 873 31.15 - 46.73: 180 46.73 - 62.30: 36 62.30 - 77.88: 8 Dihedral angle restraints: 19768 sinusoidal: 7964 harmonic: 11804 Sorted by residual: dihedral pdb=" CA PHE D 957 " pdb=" C PHE D 957 " pdb=" N ASN D 958 " pdb=" CA ASN D 958 " ideal model delta harmonic sigma weight residual 180.00 154.14 25.86 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA PHE C 957 " pdb=" C PHE C 957 " pdb=" N ASN C 958 " pdb=" CA ASN C 958 " ideal model delta harmonic sigma weight residual 180.00 154.16 25.84 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA PHE B 957 " pdb=" C PHE B 957 " pdb=" N ASN B 958 " pdb=" CA ASN B 958 " ideal model delta harmonic sigma weight residual 180.00 154.16 25.84 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 19765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3179 0.060 - 0.119: 1395 0.119 - 0.179: 226 0.179 - 0.239: 25 0.239 - 0.298: 19 Chirality restraints: 4844 Sorted by residual: chirality pdb=" CB ILE A 959 " pdb=" CA ILE A 959 " pdb=" CG1 ILE A 959 " pdb=" CG2 ILE A 959 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB ILE C 959 " pdb=" CA ILE C 959 " pdb=" CG1 ILE C 959 " pdb=" CG2 ILE C 959 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CB ILE D 959 " pdb=" CA ILE D 959 " pdb=" CG1 ILE D 959 " pdb=" CG2 ILE D 959 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 4841 not shown) Planarity restraints: 6080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D1020 " 0.026 2.00e-02 2.50e+03 2.59e-02 1.68e+01 pdb=" CG TRP D1020 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TRP D1020 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP D1020 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP D1020 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP D1020 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D1020 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP D1020 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP D1020 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D1020 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1020 " 0.027 2.00e-02 2.50e+03 2.59e-02 1.67e+01 pdb=" CG TRP B1020 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP B1020 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP B1020 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B1020 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B1020 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B1020 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1020 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1020 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B1020 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C1020 " -0.026 2.00e-02 2.50e+03 2.56e-02 1.64e+01 pdb=" CG TRP C1020 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP C1020 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP C1020 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP C1020 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP C1020 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C1020 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1020 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1020 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C1020 " -0.002 2.00e-02 2.50e+03 ... (remaining 6077 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 2183 2.62 - 3.19: 31682 3.19 - 3.76: 69100 3.76 - 4.33: 102582 4.33 - 4.90: 156266 Nonbonded interactions: 361813 Sorted by model distance: nonbonded pdb=" OE1 GLU A 461 " pdb="MG MG A2002 " model vdw 2.053 2.170 nonbonded pdb=" OE1 GLU B 461 " pdb="MG MG B2002 " model vdw 2.053 2.170 nonbonded pdb=" OE1 GLU C 461 " pdb="MG MG C2002 " model vdw 2.053 2.170 nonbonded pdb=" OE1 GLU D 461 " pdb="MG MG D2002 " model vdw 2.053 2.170 nonbonded pdb="MG MG D2002 " pdb=" O HOH D2225 " model vdw 2.066 2.170 ... (remaining 361808 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.960 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 44.850 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 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:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9078 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 : 0.012 0.125 33824 Z= 0.523 Angle : 0.924 10.521 46156 Z= 0.505 Chirality : 0.065 0.298 4844 Planarity : 0.007 0.055 6080 Dihedral : 10.160 77.881 12168 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % 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: -1.16 (0.12), residues: 4076 helix: -2.82 (0.16), residues: 500 sheet: 0.08 (0.13), residues: 1396 loop : -0.77 (0.12), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG C 881 TYR 0.043 0.004 TYR D 559 PHE 0.020 0.003 PHE C 747 TRP 0.070 0.005 TRP D1020 HIS 0.014 0.003 HIS A 464 Details of bonding type rmsd/Z covalent geometry : bond 0.01166 / 0.52 (33824) covalent geometry : angle 0.92379 / 0.50 (46156) hydrogen bonds : bond 0.20352 / 13.59 ( 1208) hydrogen bonds : angle 7.51037 / 5.16 ( 3276) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 438 time to evaluate : 1.414 Fit side-chains REVERT: A 82 ASP cc_start: 0.7820 (m-30) cc_final: 0.7509 (m-30) REVERT: A 804 ASN cc_start: 0.8872 (m110) cc_final: 0.8669 (m-40) REVERT: B 82 ASP cc_start: 0.7814 (m-30) cc_final: 0.7509 (m-30) REVERT: B 117 GLU cc_start: 0.7442 (pm20) cc_final: 0.7235 (pm20) REVERT: C 82 ASP cc_start: 0.7821 (m-30) cc_final: 0.7507 (m-30) REVERT: C 804 ASN cc_start: 0.8875 (m110) cc_final: 0.8670 (m-40) REVERT: D 82 ASP cc_start: 0.7819 (m-30) cc_final: 0.7510 (m-30) REVERT: D 804 ASN cc_start: 0.8881 (m110) cc_final: 0.8670 (m-40) outliers start: 0 outliers final: 0 residues processed: 438 average time/residue: 0.9577 time to fit residues: 488.6193 Evaluate side-chains 336 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 GLN A 646 HIS A 739 HIS ** A 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 GLN A 863 GLN A 935 ASN A 966 GLN B 266 GLN B 573 GLN B 646 HIS B 739 HIS ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 817 GLN B 863 GLN B 935 ASN B 966 GLN C 266 GLN C 646 HIS C 739 HIS ** C 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 817 GLN C 863 GLN C 935 ASN C 965 GLN C 966 GLN D 266 GLN D 646 HIS D 739 HIS ** D 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 817 GLN D 863 GLN D 935 ASN D 966 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.094886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.074029 restraints weight = 47917.517| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.78 r_work: 0.2813 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9292 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 33824 Z= 0.115 Angle : 0.565 12.293 46156 Z= 0.293 Chirality : 0.045 0.152 4844 Planarity : 0.004 0.036 6080 Dihedral : 5.529 59.834 4480 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.63 % Allowed : 4.70 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % 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: -0.31 (0.13), residues: 4076 helix: -1.14 (0.20), residues: 532 sheet: 0.47 (0.13), residues: 1332 loop : -0.31 (0.13), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 251 TYR 0.017 0.001 TYR B 100 PHE 0.016 0.001 PHE B 549 TRP 0.029 0.002 TRP D 553 HIS 0.006 0.001 HIS B 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (33824) covalent geometry : angle 0.56543 / 0.29 (46156) hydrogen bonds : bond 0.04196 / 2.84 ( 1208) hydrogen bonds : angle 5.35303 / 3.73 ( 3276) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 401 time to evaluate : 1.371 Fit side-chains REVERT: A 438 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8534 (mt-10) REVERT: A 965 GLN cc_start: 0.8966 (tt0) cc_final: 0.8733 (tt0) REVERT: B 46 ARG cc_start: 0.8542 (mtm-85) cc_final: 0.8239 (mtm-85) REVERT: B 128 ASN cc_start: 0.8805 (OUTLIER) cc_final: 0.8485 (t0) REVERT: B 438 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8500 (mt-10) REVERT: B 965 GLN cc_start: 0.8967 (tt0) cc_final: 0.8739 (tt0) REVERT: C 438 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8535 (mt-10) REVERT: D 46 ARG cc_start: 0.8535 (mtm-85) cc_final: 0.8232 (mtm-85) REVERT: D 128 ASN cc_start: 0.8803 (OUTLIER) cc_final: 0.8423 (t0) REVERT: D 438 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8504 (mt-10) REVERT: D 965 GLN cc_start: 0.8956 (tt0) cc_final: 0.8723 (tt0) outliers start: 22 outliers final: 8 residues processed: 413 average time/residue: 0.9285 time to fit residues: 449.3215 Evaluate side-chains 343 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 333 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 515 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 107 optimal weight: 9.9990 chunk 168 optimal weight: 0.9990 chunk 257 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 406 optimal weight: 10.0000 chunk 219 optimal weight: 10.0000 chunk 277 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN A 262 GLN A 563 GLN A 573 GLN A 783 GLN A 817 GLN A 863 GLN A 945 ASN B 12 GLN B 262 GLN B 563 GLN B 783 GLN B 817 GLN B 863 GLN B 945 ASN C 12 GLN C 262 GLN C 563 GLN C 573 GLN C 783 GLN C 817 GLN C 863 GLN C 945 ASN C 965 GLN D 12 GLN D 262 GLN D 563 GLN D 573 GLN D 783 GLN D 817 GLN D 863 GLN D 945 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.090317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.068384 restraints weight = 48033.782| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 1.80 r_work: 0.2694 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9352 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 : 0.006 0.049 33824 Z= 0.268 Angle : 0.644 12.147 46156 Z= 0.336 Chirality : 0.048 0.185 4844 Planarity : 0.004 0.032 6080 Dihedral : 5.737 58.723 4480 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.80 % Allowed : 6.36 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % 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: 0.18 (0.13), residues: 4076 helix: -0.42 (0.21), residues: 532 sheet: 0.77 (0.14), residues: 1356 loop : -0.06 (0.13), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 166 TYR 0.021 0.002 TYR D 100 PHE 0.013 0.002 PHE B 989 TRP 0.032 0.002 TRP A 553 HIS 0.008 0.002 HIS D 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.27 (33824) covalent geometry : angle 0.64423 / 0.34 (46156) hydrogen bonds : bond 0.04972 / 3.33 ( 1208) hydrogen bonds : angle 5.42983 / 3.77 ( 3276) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 365 time to evaluate : 1.518 Fit side-chains REVERT: A 128 ASN cc_start: 0.8764 (t0) cc_final: 0.8542 (t0) REVERT: B 128 ASN cc_start: 0.8820 (m110) cc_final: 0.8493 (t0) REVERT: C 128 ASN cc_start: 0.8759 (t0) cc_final: 0.8536 (t0) REVERT: C 438 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8598 (mt-10) REVERT: D 128 ASN cc_start: 0.8812 (m110) cc_final: 0.8492 (t0) outliers start: 28 outliers final: 16 residues processed: 389 average time/residue: 0.9392 time to fit residues: 428.0430 Evaluate side-chains 356 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 340 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 855 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 296 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 405 optimal weight: 4.9990 chunk 375 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 chunk 228 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 385 optimal weight: 2.9990 chunk 287 optimal weight: 5.9990 chunk 316 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 634 GLN A 739 HIS A 844 HIS A 863 GLN B 634 GLN B 739 HIS B 844 HIS B 863 GLN C 634 GLN C 739 HIS C 844 HIS C 863 GLN D 634 GLN D 739 HIS D 844 HIS D 863 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.092179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.070822 restraints weight = 47797.129| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 1.78 r_work: 0.2739 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9330 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33824 Z= 0.159 Angle : 0.569 11.362 46156 Z= 0.296 Chirality : 0.045 0.170 4844 Planarity : 0.004 0.030 6080 Dihedral : 5.458 58.957 4480 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.83 % Allowed : 6.90 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % 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: 0.41 (0.13), residues: 4076 helix: 0.26 (0.22), residues: 508 sheet: 0.85 (0.14), residues: 1336 loop : 0.01 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 251 TYR 0.019 0.001 TYR C 100 PHE 0.010 0.001 PHE C 549 TRP 0.033 0.002 TRP A 553 HIS 0.007 0.001 HIS C 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (33824) covalent geometry : angle 0.56920 / 0.30 (46156) hydrogen bonds : bond 0.04083 / 2.75 ( 1208) hydrogen bonds : angle 5.22269 / 3.64 ( 3276) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 364 time to evaluate : 1.515 Fit side-chains REVERT: A 2 MET cc_start: 0.8014 (tpp) cc_final: 0.7736 (tpt) REVERT: A 128 ASN cc_start: 0.8714 (t0) cc_final: 0.8471 (t0) REVERT: A 136 GLU cc_start: 0.8504 (pm20) cc_final: 0.8202 (pt0) REVERT: A 634 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8687 (tp40) REVERT: B 2 MET cc_start: 0.8024 (tpp) cc_final: 0.7745 (tpt) REVERT: B 128 ASN cc_start: 0.8800 (m110) cc_final: 0.8396 (t0) REVERT: B 136 GLU cc_start: 0.8517 (pm20) cc_final: 0.8215 (pt0) REVERT: C 2 MET cc_start: 0.8012 (tpp) cc_final: 0.7712 (tpt) REVERT: C 128 ASN cc_start: 0.8712 (t0) cc_final: 0.8474 (t0) REVERT: C 136 GLU cc_start: 0.8516 (pm20) cc_final: 0.8207 (pt0) REVERT: C 634 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8646 (tp40) REVERT: D 2 MET cc_start: 0.8001 (tpp) cc_final: 0.7717 (tpt) REVERT: D 128 ASN cc_start: 0.8798 (m110) cc_final: 0.8396 (t0) REVERT: D 136 GLU cc_start: 0.8512 (pm20) cc_final: 0.8214 (pt0) outliers start: 29 outliers final: 16 residues processed: 384 average time/residue: 0.9336 time to fit residues: 420.4940 Evaluate side-chains 356 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 338 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 634 GLN Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 634 GLN Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 855 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 139 optimal weight: 0.9990 chunk 287 optimal weight: 9.9990 chunk 250 optimal weight: 10.0000 chunk 329 optimal weight: 0.6980 chunk 201 optimal weight: 8.9990 chunk 130 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 368 optimal weight: 9.9990 chunk 389 optimal weight: 9.9990 chunk 403 optimal weight: 9.9990 chunk 291 optimal weight: 0.8980 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN A 739 HIS A 817 GLN A 863 GLN B 394 ASN B 634 GLN B 739 HIS B 817 GLN B 863 GLN C 394 ASN C 634 GLN C 739 HIS C 817 GLN C 863 GLN D 394 ASN D 634 GLN D 739 HIS D 817 GLN D 863 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.090563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.068529 restraints weight = 47595.912| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 1.80 r_work: 0.2694 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9352 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 33824 Z= 0.241 Angle : 0.618 10.998 46156 Z= 0.323 Chirality : 0.048 0.181 4844 Planarity : 0.004 0.031 6080 Dihedral : 5.645 58.230 4480 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.72 % Allowed : 7.45 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % 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: 0.48 (0.13), residues: 4076 helix: 0.24 (0.22), residues: 508 sheet: 0.87 (0.14), residues: 1384 loop : 0.08 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 251 TYR 0.022 0.002 TYR C 100 PHE 0.011 0.001 PHE C 989 TRP 0.034 0.002 TRP B 553 HIS 0.008 0.001 HIS D 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.24 (33824) covalent geometry : angle 0.61828 / 0.32 (46156) hydrogen bonds : bond 0.04614 / 3.09 ( 1208) hydrogen bonds : angle 5.33769 / 3.71 ( 3276) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 351 time to evaluate : 1.334 Fit side-chains REVERT: A 2 MET cc_start: 0.7953 (tpp) cc_final: 0.7615 (tpt) REVERT: A 117 GLU cc_start: 0.8172 (mp0) cc_final: 0.7799 (pm20) REVERT: A 128 ASN cc_start: 0.8742 (t0) cc_final: 0.8513 (t0) REVERT: A 819 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7821 (pm20) REVERT: B 2 MET cc_start: 0.7951 (tpp) cc_final: 0.7615 (tpt) REVERT: B 128 ASN cc_start: 0.8810 (m110) cc_final: 0.8407 (t0) REVERT: B 634 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8682 (tp40) REVERT: B 819 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7819 (pm20) REVERT: C 2 MET cc_start: 0.7979 (tpp) cc_final: 0.7666 (tpt) REVERT: C 128 ASN cc_start: 0.8744 (t0) cc_final: 0.8513 (t0) REVERT: D 2 MET cc_start: 0.7966 (tpp) cc_final: 0.7622 (tpt) REVERT: D 128 ASN cc_start: 0.8806 (OUTLIER) cc_final: 0.8405 (t0) REVERT: D 634 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8627 (tp40) outliers start: 25 outliers final: 16 residues processed: 371 average time/residue: 0.9025 time to fit residues: 392.3659 Evaluate side-chains 361 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 342 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 634 GLN Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 634 GLN Chi-restraints excluded: chain D residue 855 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 219 optimal weight: 6.9990 chunk 213 optimal weight: 0.7980 chunk 320 optimal weight: 7.9990 chunk 333 optimal weight: 0.8980 chunk 266 optimal weight: 7.9990 chunk 398 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 212 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 381 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 634 GLN A 739 HIS A 817 GLN A 863 GLN ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS B 817 GLN B 863 GLN ** B 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 634 GLN C 739 HIS C 817 GLN C 863 GLN ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 HIS D 817 GLN D 863 GLN ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.095439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.074337 restraints weight = 47455.210| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.77 r_work: 0.2814 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9287 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 33824 Z= 0.100 Angle : 0.519 10.903 46156 Z= 0.268 Chirality : 0.043 0.162 4844 Planarity : 0.003 0.029 6080 Dihedral : 5.107 59.561 4480 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.86 % Allowed : 7.70 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % 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: 0.56 (0.13), residues: 4076 helix: 0.70 (0.23), residues: 512 sheet: 0.98 (0.14), residues: 1324 loop : -0.00 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 251 TYR 0.017 0.001 TYR C 100 PHE 0.010 0.001 PHE A 758 TRP 0.034 0.001 TRP B 553 HIS 0.005 0.001 HIS C 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (33824) covalent geometry : angle 0.51890 / 0.27 (46156) hydrogen bonds : bond 0.03269 / 2.20 ( 1208) hydrogen bonds : angle 4.96207 / 3.46 ( 3276) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 378 time to evaluate : 1.509 Fit side-chains REVERT: A 2 MET cc_start: 0.7964 (tpp) cc_final: 0.7611 (tpt) REVERT: A 117 GLU cc_start: 0.8240 (mp0) cc_final: 0.7896 (pm20) REVERT: A 136 GLU cc_start: 0.8532 (pm20) cc_final: 0.8305 (pm20) REVERT: A 965 GLN cc_start: 0.8956 (tt0) cc_final: 0.8710 (tt0) REVERT: B 2 MET cc_start: 0.7968 (tpp) cc_final: 0.7616 (tpt) REVERT: B 136 GLU cc_start: 0.8545 (pm20) cc_final: 0.8312 (pm20) REVERT: B 965 GLN cc_start: 0.8960 (tt0) cc_final: 0.8717 (tt0) REVERT: C 2 MET cc_start: 0.7969 (tpp) cc_final: 0.7600 (tpt) REVERT: C 117 GLU cc_start: 0.8231 (mp0) cc_final: 0.7926 (pm20) REVERT: C 136 GLU cc_start: 0.8535 (pm20) cc_final: 0.8309 (pm20) REVERT: C 965 GLN cc_start: 0.8963 (tt0) cc_final: 0.8730 (tt0) REVERT: D 2 MET cc_start: 0.7955 (tpp) cc_final: 0.7593 (tpt) REVERT: D 117 GLU cc_start: 0.8234 (mp0) cc_final: 0.7931 (pm20) REVERT: D 136 GLU cc_start: 0.8535 (pm20) cc_final: 0.8307 (pm20) REVERT: D 965 GLN cc_start: 0.8957 (tt0) cc_final: 0.8721 (tt0) outliers start: 30 outliers final: 16 residues processed: 396 average time/residue: 0.9116 time to fit residues: 424.4683 Evaluate side-chains 362 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 346 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 855 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 16 optimal weight: 4.9990 chunk 277 optimal weight: 0.0670 chunk 14 optimal weight: 0.8980 chunk 283 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 354 optimal weight: 9.9990 chunk 349 optimal weight: 6.9990 chunk 212 optimal weight: 0.7980 chunk 398 optimal weight: 0.0870 chunk 214 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 634 GLN A 739 HIS A 896 ASN ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 634 GLN B 739 HIS B 896 ASN ** B 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 634 GLN C 739 HIS C 817 GLN C 896 ASN ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 634 GLN D 739 HIS D 896 ASN ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.097334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.076515 restraints weight = 47515.695| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.77 r_work: 0.2856 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9266 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 33824 Z= 0.089 Angle : 0.502 9.646 46156 Z= 0.258 Chirality : 0.043 0.165 4844 Planarity : 0.003 0.029 6080 Dihedral : 4.892 58.785 4480 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.57 % Allowed : 8.59 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % 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: 0.65 (0.13), residues: 4076 helix: 0.87 (0.24), residues: 512 sheet: 1.03 (0.14), residues: 1328 loop : 0.03 (0.13), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 251 TYR 0.017 0.001 TYR A 100 PHE 0.011 0.001 PHE C 225 TRP 0.030 0.001 TRP A 553 HIS 0.003 0.000 HIS C 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.09 (33824) covalent geometry : angle 0.50155 / 0.26 (46156) hydrogen bonds : bond 0.03028 / 2.03 ( 1208) hydrogen bonds : angle 4.79735 / 3.34 ( 3276) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 391 time to evaluate : 1.367 Fit side-chains REVERT: A 2 MET cc_start: 0.7982 (tpp) cc_final: 0.7636 (tpt) REVERT: A 117 GLU cc_start: 0.8229 (mp0) cc_final: 0.7891 (pm20) REVERT: A 128 ASN cc_start: 0.8648 (t0) cc_final: 0.8296 (m-40) REVERT: A 271 THR cc_start: 0.9183 (t) cc_final: 0.8932 (m) REVERT: A 438 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8443 (mt-10) REVERT: B 2 MET cc_start: 0.7983 (tpp) cc_final: 0.7637 (tpt) REVERT: B 46 ARG cc_start: 0.8493 (mtm-85) cc_final: 0.8241 (mtm-85) REVERT: B 271 THR cc_start: 0.9199 (t) cc_final: 0.8935 (m) REVERT: B 438 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8450 (mt-10) REVERT: C 2 MET cc_start: 0.7976 (tpp) cc_final: 0.7600 (tpt) REVERT: C 117 GLU cc_start: 0.8218 (mp0) cc_final: 0.7901 (pm20) REVERT: C 128 ASN cc_start: 0.8644 (t0) cc_final: 0.8291 (m-40) REVERT: C 271 THR cc_start: 0.9189 (t) cc_final: 0.8919 (m) REVERT: C 438 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8449 (mt-10) REVERT: D 2 MET cc_start: 0.7960 (tpp) cc_final: 0.7598 (tpt) REVERT: D 46 ARG cc_start: 0.8483 (mtm-85) cc_final: 0.8232 (mtm-85) REVERT: D 117 GLU cc_start: 0.8221 (mp0) cc_final: 0.7904 (pm20) REVERT: D 271 THR cc_start: 0.9181 (t) cc_final: 0.8914 (m) REVERT: D 438 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8444 (mt-10) outliers start: 20 outliers final: 16 residues processed: 407 average time/residue: 0.9182 time to fit residues: 438.0009 Evaluate side-chains 372 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 356 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 855 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 278 optimal weight: 20.0000 chunk 229 optimal weight: 0.9990 chunk 295 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 292 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 239 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN A 634 GLN A 739 HIS A 817 GLN B 262 GLN B 634 GLN B 739 HIS B 817 GLN C 262 GLN C 634 GLN C 739 HIS C 817 GLN D 262 GLN D 634 GLN D 739 HIS D 817 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.092380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.070690 restraints weight = 47201.168| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.79 r_work: 0.2739 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9329 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33824 Z= 0.179 Angle : 0.575 9.664 46156 Z= 0.299 Chirality : 0.045 0.168 4844 Planarity : 0.004 0.032 6080 Dihedral : 5.298 58.094 4480 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.89 % Allowed : 8.82 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % 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: 0.65 (0.13), residues: 4076 helix: 0.69 (0.23), residues: 508 sheet: 0.97 (0.14), residues: 1388 loop : 0.11 (0.14), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 251 TYR 0.020 0.002 TYR A 100 PHE 0.011 0.001 PHE D 225 TRP 0.025 0.001 TRP C 553 HIS 0.006 0.001 HIS D 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (33824) covalent geometry : angle 0.57529 / 0.30 (46156) hydrogen bonds : bond 0.04014 / 2.69 ( 1208) hydrogen bonds : angle 5.09142 / 3.54 ( 3276) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 364 time to evaluate : 1.477 Fit side-chains REVERT: A 2 MET cc_start: 0.7992 (tpp) cc_final: 0.7594 (tpt) REVERT: A 117 GLU cc_start: 0.8190 (mp0) cc_final: 0.7846 (pm20) REVERT: A 128 ASN cc_start: 0.8729 (t0) cc_final: 0.8470 (t0) REVERT: A 819 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.7087 (pm20) REVERT: B 2 MET cc_start: 0.7992 (tpp) cc_final: 0.7596 (tpt) REVERT: B 819 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7113 (pm20) REVERT: C 2 MET cc_start: 0.8018 (tpp) cc_final: 0.7653 (tpt) REVERT: C 117 GLU cc_start: 0.8188 (mp0) cc_final: 0.7827 (pm20) REVERT: C 128 ASN cc_start: 0.8718 (t0) cc_final: 0.8459 (t0) REVERT: D 2 MET cc_start: 0.7995 (tpp) cc_final: 0.7588 (tpt) REVERT: D 117 GLU cc_start: 0.8195 (mp0) cc_final: 0.7838 (pm20) outliers start: 31 outliers final: 18 residues processed: 382 average time/residue: 0.9282 time to fit residues: 416.0178 Evaluate side-chains 367 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 347 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 819 GLU Chi-restraints excluded: chain D residue 855 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 91 optimal weight: 9.9990 chunk 336 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 221 optimal weight: 5.9990 chunk 274 optimal weight: 4.9990 chunk 194 optimal weight: 0.7980 chunk 202 optimal weight: 0.1980 chunk 131 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 345 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN A 634 GLN A 739 HIS A 817 GLN B 262 GLN B 634 GLN B 739 HIS B 817 GLN C 262 GLN C 634 GLN C 739 HIS C 817 GLN D 262 GLN D 634 GLN D 739 HIS D 817 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.094943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.073526 restraints weight = 47301.414| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.79 r_work: 0.2798 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9298 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 33824 Z= 0.107 Angle : 0.528 9.975 46156 Z= 0.272 Chirality : 0.043 0.166 4844 Planarity : 0.003 0.035 6080 Dihedral : 5.088 59.062 4480 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.69 % Allowed : 8.99 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % 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: 0.67 (0.13), residues: 4076 helix: 0.77 (0.23), residues: 512 sheet: 1.04 (0.14), residues: 1340 loop : 0.06 (0.14), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 251 TYR 0.018 0.001 TYR D 100 PHE 0.009 0.001 PHE A 758 TRP 0.029 0.001 TRP C 553 HIS 0.004 0.001 HIS D 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (33824) covalent geometry : angle 0.52758 / 0.27 (46156) hydrogen bonds : bond 0.03356 / 2.25 ( 1208) hydrogen bonds : angle 4.93159 / 3.43 ( 3276) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 353 time to evaluate : 1.435 Fit side-chains REVERT: A 2 MET cc_start: 0.7990 (tpp) cc_final: 0.7590 (tpt) REVERT: A 117 GLU cc_start: 0.8205 (mp0) cc_final: 0.7848 (pm20) REVERT: A 262 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8331 (tt0) REVERT: B 2 MET cc_start: 0.7992 (tpp) cc_final: 0.7596 (tpt) REVERT: B 262 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8317 (tt0) REVERT: C 2 MET cc_start: 0.8004 (tpp) cc_final: 0.7584 (tpt) REVERT: C 117 GLU cc_start: 0.8196 (mp0) cc_final: 0.7845 (pm20) REVERT: C 262 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8336 (tt0) REVERT: D 2 MET cc_start: 0.7998 (tpp) cc_final: 0.7588 (tpt) REVERT: D 117 GLU cc_start: 0.8207 (mp0) cc_final: 0.7859 (pm20) REVERT: D 262 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8315 (tt0) outliers start: 24 outliers final: 17 residues processed: 369 average time/residue: 0.9610 time to fit residues: 414.8998 Evaluate side-chains 365 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 344 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 855 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 83 optimal weight: 9.9990 chunk 195 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 312 optimal weight: 3.9990 chunk 372 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 238 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN A 634 GLN A 817 GLN B 262 GLN B 634 GLN B 817 GLN C 262 GLN C 634 GLN C 739 HIS C 817 GLN D 262 GLN D 634 GLN D 817 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.091745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.069950 restraints weight = 47363.768| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 1.80 r_work: 0.2725 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9337 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 33824 Z= 0.206 Angle : 0.599 9.808 46156 Z= 0.311 Chirality : 0.046 0.178 4844 Planarity : 0.004 0.031 6080 Dihedral : 5.385 58.021 4480 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.86 % Allowed : 8.71 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % 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: 0.68 (0.13), residues: 4076 helix: 0.61 (0.23), residues: 508 sheet: 0.97 (0.14), residues: 1376 loop : 0.18 (0.14), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 251 TYR 0.022 0.002 TYR A 100 PHE 0.011 0.001 PHE B 225 TRP 0.022 0.002 TRP D 553 HIS 0.006 0.001 HIS C 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.21 (33824) covalent geometry : angle 0.59881 / 0.31 (46156) hydrogen bonds : bond 0.04161 / 2.79 ( 1208) hydrogen bonds : angle 5.13488 / 3.56 ( 3276) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 353 time to evaluate : 1.565 Fit side-chains REVERT: A 2 MET cc_start: 0.8000 (tpp) cc_final: 0.7625 (tpt) REVERT: A 117 GLU cc_start: 0.8186 (mp0) cc_final: 0.7837 (pm20) REVERT: A 128 ASN cc_start: 0.8744 (t0) cc_final: 0.8502 (t0) REVERT: A 262 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8391 (tt0) REVERT: B 2 MET cc_start: 0.7990 (tpp) cc_final: 0.7617 (tpt) REVERT: B 128 ASN cc_start: 0.8799 (m110) cc_final: 0.8432 (t0) REVERT: B 262 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8393 (tt0) REVERT: C 2 MET cc_start: 0.8011 (tpp) cc_final: 0.7606 (tpt) REVERT: C 117 GLU cc_start: 0.8174 (mp0) cc_final: 0.7808 (pm20) REVERT: C 128 ASN cc_start: 0.8738 (t0) cc_final: 0.8491 (t0) REVERT: C 262 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8395 (tt0) REVERT: D 2 MET cc_start: 0.8014 (tpp) cc_final: 0.7625 (tpt) REVERT: D 117 GLU cc_start: 0.8192 (mp0) cc_final: 0.7827 (pm20) REVERT: D 128 ASN cc_start: 0.8797 (m110) cc_final: 0.8409 (t0) REVERT: D 262 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8391 (tt0) outliers start: 30 outliers final: 16 residues processed: 375 average time/residue: 0.9322 time to fit residues: 410.5930 Evaluate side-chains 365 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 345 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 855 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 323 optimal weight: 5.9990 chunk 185 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 277 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 291 optimal weight: 3.9990 chunk 324 optimal weight: 5.9990 chunk 358 optimal weight: 6.9990 chunk 213 optimal weight: 3.9990 chunk 394 optimal weight: 8.9990 chunk 357 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN A 634 GLN A 739 HIS A 817 GLN B 262 GLN B 418 HIS B 739 HIS B 817 GLN C 262 GLN C 634 GLN C 739 HIS C 817 GLN C 863 GLN D 262 GLN D 418 HIS D 739 HIS D 817 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.091498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.069727 restraints weight = 47251.126| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 1.79 r_work: 0.2719 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9339 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 33824 Z= 0.208 Angle : 0.604 10.733 46156 Z= 0.314 Chirality : 0.046 0.180 4844 Planarity : 0.004 0.030 6080 Dihedral : 5.480 58.236 4480 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.66 % Allowed : 8.93 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % 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: 0.66 (0.13), residues: 4076 helix: 0.54 (0.23), residues: 508 sheet: 0.94 (0.14), residues: 1376 loop : 0.19 (0.14), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 251 TYR 0.022 0.002 TYR A 100 PHE 0.010 0.001 PHE A 225 TRP 0.024 0.002 TRP A 553 HIS 0.006 0.001 HIS D 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.21 (33824) covalent geometry : angle 0.60391 / 0.31 (46156) hydrogen bonds : bond 0.04214 / 2.83 ( 1208) hydrogen bonds : angle 5.19069 / 3.61 ( 3276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19305.05 seconds wall clock time: 328 minutes 6.72 seconds (19686.72 seconds total)