Starting phenix.real_space_refine on Tue Aug 26 12:12:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cvm_7770/08_2025/6cvm_7770.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cvm_7770/08_2025/6cvm_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_7770/08_2025/6cvm_7770.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cvm_7770/08_2025/6cvm_7770.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6cvm_7770/08_2025/6cvm_7770.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cvm_7770/08_2025/6cvm_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 10.98, per 1000 atoms: 0.30 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: 3.54 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.69 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: 12.39 Time building geometry restraints manager: 4.64 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: 18759 15.58 - 31.15: 873 31.15 - 46.73: 180 46.73 - 62.30: 44 62.30 - 77.88: 8 Dihedral angle restraints: 19864 sinusoidal: 8060 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 19861 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: 0.10 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: 3.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.880 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 42.430 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 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 : 10.251 77.881 12264 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 aren 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 covalent geometry : bond 0.01166 (33824) covalent geometry : angle 0.92379 (46156) hydrogen bonds : bond 0.20352 ( 1208) hydrogen bonds : angle 7.51037 ( 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 : 1.367 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: 0.8940 time to fit residues: 453.6584 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 : 1.358 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 12 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: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.094550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.073339 restraints weight = 47821.316| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.79 r_work: 0.2798 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9120 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 33824 Z= 0.119 Angle : 0.573 12.011 46156 Z= 0.298 Chirality : 0.045 0.152 4844 Planarity : 0.004 0.037 6080 Dihedral : 6.042 59.223 4576 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.63 % Allowed : 4.90 % Favored : 94.47 % 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 aren not related in a simple way. whole: -0.33 (0.13), residues: 4076 helix: -1.18 (0.20), residues: 532 sheet: 0.48 (0.13), residues: 1324 loop : -0.32 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 251 TYR 0.018 0.001 TYR A 100 PHE 0.016 0.001 PHE A 549 TRP 0.030 0.002 TRP D 553 HIS 0.006 0.001 HIS D 395 Details of bonding type rmsd covalent geometry : bond 0.00246 (33824) covalent geometry : angle 0.57317 (46156) hydrogen bonds : bond 0.04434 ( 1208) hydrogen bonds : angle 5.40537 ( 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 418 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 396 time to evaluate : 1.079 Fit side-chains REVERT: A 128 ASN cc_start: 0.8780 (t0) cc_final: 0.8437 (t0) REVERT: A 438 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8498 (mt-10) REVERT: A 965 GLN cc_start: 0.8983 (tt0) cc_final: 0.8747 (tt0) REVERT: B 46 ARG cc_start: 0.8519 (mtm-85) cc_final: 0.8223 (mtm-85) REVERT: B 82 ASP cc_start: 0.8530 (m-30) cc_final: 0.8324 (m-30) REVERT: B 128 ASN cc_start: 0.8806 (OUTLIER) cc_final: 0.8479 (t0) REVERT: B 438 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8484 (mt-10) REVERT: B 965 GLN cc_start: 0.8984 (tt0) cc_final: 0.8749 (tt0) REVERT: C 82 ASP cc_start: 0.8546 (m-30) cc_final: 0.8343 (m-30) REVERT: C 128 ASN cc_start: 0.8768 (t0) cc_final: 0.8449 (t0) REVERT: C 438 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8489 (mt-10) REVERT: D 46 ARG cc_start: 0.8513 (mtm-85) cc_final: 0.8223 (mtm-85) REVERT: D 82 ASP cc_start: 0.8536 (m-30) cc_final: 0.8334 (m-30) REVERT: D 128 ASN cc_start: 0.8811 (OUTLIER) cc_final: 0.8485 (t0) REVERT: D 438 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8482 (mt-10) REVERT: D 965 GLN cc_start: 0.8968 (tt0) cc_final: 0.8728 (tt0) outliers start: 22 outliers final: 4 residues processed: 408 average time/residue: 0.8638 time to fit residues: 410.2446 Evaluate side-chains 343 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 337 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain C residue 515 VAL 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: 10.0000 chunk 168 optimal weight: 2.9990 chunk 257 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 27 optimal weight: 0.0000 chunk 116 optimal weight: 9.9990 chunk 406 optimal weight: 10.0000 chunk 219 optimal weight: 9.9990 chunk 277 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 overall best weight: 3.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 262 GLN A 563 GLN A 573 GLN A 739 HIS A 783 GLN A 817 GLN A 863 GLN A 945 ASN 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 739 HIS 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 739 HIS D 783 GLN D 817 GLN D 863 GLN D 945 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.091000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.069118 restraints weight = 48000.752| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 1.81 r_work: 0.2708 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9172 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 33824 Z= 0.230 Angle : 0.621 12.152 46156 Z= 0.324 Chirality : 0.047 0.181 4844 Planarity : 0.004 0.031 6080 Dihedral : 6.162 59.617 4576 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.72 % Allowed : 6.50 % Favored : 92.78 % 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 aren not related in a simple way. whole: 0.20 (0.13), residues: 4076 helix: -0.16 (0.21), residues: 508 sheet: 0.73 (0.14), residues: 1356 loop : -0.09 (0.13), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 251 TYR 0.020 0.002 TYR D 100 PHE 0.012 0.002 PHE A 549 TRP 0.031 0.002 TRP D 553 HIS 0.008 0.001 HIS B 395 Details of bonding type rmsd covalent geometry : bond 0.00510 (33824) covalent geometry : angle 0.62109 (46156) hydrogen bonds : bond 0.04761 ( 1208) hydrogen bonds : angle 5.38445 ( 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 395 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 370 time to evaluate : 0.909 Fit side-chains REVERT: A 128 ASN cc_start: 0.8773 (t0) cc_final: 0.8556 (t0) REVERT: A 243 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.7842 (tm-30) REVERT: A 438 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8612 (mt-10) REVERT: A 634 GLN cc_start: 0.8996 (mm-40) cc_final: 0.8668 (tp40) REVERT: B 82 ASP cc_start: 0.8531 (m-30) cc_final: 0.8307 (m-30) REVERT: B 128 ASN cc_start: 0.8815 (m110) cc_final: 0.8487 (t0) REVERT: B 438 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8607 (mt-10) REVERT: B 634 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8669 (tp40) REVERT: C 82 ASP cc_start: 0.8515 (m-30) cc_final: 0.8288 (m-30) REVERT: C 128 ASN cc_start: 0.8772 (t0) cc_final: 0.8555 (t0) REVERT: C 438 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8605 (mt-10) REVERT: C 634 GLN cc_start: 0.9003 (mm-40) cc_final: 0.8677 (tp40) REVERT: D 82 ASP cc_start: 0.8525 (m-30) cc_final: 0.8300 (m-30) REVERT: D 128 ASN cc_start: 0.8814 (m110) cc_final: 0.8492 (t0) REVERT: D 438 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8603 (mt-10) outliers start: 25 outliers final: 16 residues processed: 386 average time/residue: 0.8334 time to fit residues: 375.7495 Evaluate side-chains 364 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 347 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 243 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: 9.9990 chunk 375 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 chunk 228 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 385 optimal weight: 0.9990 chunk 287 optimal weight: 8.9990 chunk 316 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 739 HIS A 817 GLN A 863 GLN B 739 HIS B 817 GLN B 863 GLN C 739 HIS C 817 GLN C 863 GLN D 634 GLN D 739 HIS D 817 GLN D 863 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.092187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.070266 restraints weight = 47575.339| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 1.81 r_work: 0.2730 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9158 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 33824 Z= 0.174 Angle : 0.578 11.119 46156 Z= 0.301 Chirality : 0.046 0.176 4844 Planarity : 0.004 0.029 6080 Dihedral : 5.979 59.103 4576 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.95 % Allowed : 6.59 % Favored : 92.47 % 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 aren not related in a simple way. whole: 0.41 (0.13), residues: 4076 helix: 0.24 (0.22), residues: 508 sheet: 0.84 (0.14), residues: 1356 loop : 0.01 (0.13), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 251 TYR 0.020 0.002 TYR D 100 PHE 0.012 0.001 PHE D 758 TRP 0.033 0.002 TRP C 553 HIS 0.007 0.001 HIS C 395 Details of bonding type rmsd covalent geometry : bond 0.00383 (33824) covalent geometry : angle 0.57816 (46156) hydrogen bonds : bond 0.04189 ( 1208) hydrogen bonds : angle 5.23170 ( 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 405 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 372 time to evaluate : 1.480 Fit side-chains REVERT: A 2 MET cc_start: 0.8013 (tpp) cc_final: 0.7743 (tpt) REVERT: A 136 GLU cc_start: 0.8531 (pm20) cc_final: 0.8231 (pt0) REVERT: A 634 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8671 (tp40) REVERT: B 2 MET cc_start: 0.8035 (tpp) cc_final: 0.7763 (tpt) REVERT: B 128 ASN cc_start: 0.8802 (m110) cc_final: 0.8397 (t0) REVERT: B 136 GLU cc_start: 0.8524 (pm20) cc_final: 0.8226 (pt0) REVERT: B 634 GLN cc_start: 0.8985 (mm-40) cc_final: 0.8691 (tp40) REVERT: C 2 MET cc_start: 0.8011 (tpp) cc_final: 0.7740 (tpt) REVERT: C 136 GLU cc_start: 0.8543 (pm20) cc_final: 0.8239 (pt0) REVERT: C 819 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7838 (pm20) REVERT: D 2 MET cc_start: 0.8032 (tpp) cc_final: 0.7760 (tpt) REVERT: D 128 ASN cc_start: 0.8808 (m110) cc_final: 0.8402 (t0) REVERT: D 136 GLU cc_start: 0.8535 (pm20) cc_final: 0.8228 (pt0) REVERT: D 634 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8676 (tp40) outliers start: 33 outliers final: 16 residues processed: 396 average time/residue: 0.8462 time to fit residues: 391.8310 Evaluate side-chains 359 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 342 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 634 GLN 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: 0.8980 chunk 287 optimal weight: 5.9990 chunk 250 optimal weight: 9.9990 chunk 329 optimal weight: 10.0000 chunk 201 optimal weight: 0.7980 chunk 130 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 368 optimal weight: 8.9990 chunk 389 optimal weight: 5.9990 chunk 403 optimal weight: 9.9990 chunk 291 optimal weight: 6.9990 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN A 394 ASN A 739 HIS A 817 GLN A 863 GLN B 262 GLN B 394 ASN B 739 HIS B 817 GLN B 863 GLN C 262 GLN C 394 ASN C 634 GLN C 739 HIS C 817 GLN C 863 GLN D 262 GLN D 394 ASN D 634 GLN D 739 HIS D 817 GLN D 863 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.090679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.068641 restraints weight = 47586.243| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 1.80 r_work: 0.2696 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9175 moved from start: 0.1662 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= 0.233 Angle : 0.613 11.653 46156 Z= 0.321 Chirality : 0.047 0.185 4844 Planarity : 0.004 0.031 6080 Dihedral : 6.140 59.585 4576 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.72 % Allowed : 7.13 % Favored : 92.15 % 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 aren not related in a simple way. whole: 0.48 (0.13), residues: 4076 helix: 0.25 (0.22), residues: 508 sheet: 0.86 (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 B 251 TYR 0.022 0.002 TYR C 100 PHE 0.010 0.001 PHE D 989 TRP 0.034 0.002 TRP D 553 HIS 0.008 0.001 HIS D 395 Details of bonding type rmsd covalent geometry : bond 0.00515 (33824) covalent geometry : angle 0.61349 (46156) hydrogen bonds : bond 0.04567 ( 1208) hydrogen bonds : angle 5.32057 ( 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 392 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 367 time to evaluate : 1.248 Fit side-chains REVERT: A 2 MET cc_start: 0.7942 (tpp) cc_final: 0.7623 (tpt) REVERT: A 128 ASN cc_start: 0.8758 (t0) cc_final: 0.8528 (t0) REVERT: A 634 GLN cc_start: 0.8959 (mm-40) cc_final: 0.8638 (tp40) REVERT: A 819 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7795 (pm20) REVERT: B 2 MET cc_start: 0.7948 (tpp) cc_final: 0.7628 (tpt) REVERT: B 128 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.8402 (t0) REVERT: B 634 GLN cc_start: 0.8958 (mm-40) cc_final: 0.8636 (tp40) REVERT: B 819 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7800 (pm20) REVERT: C 2 MET cc_start: 0.7940 (tpp) cc_final: 0.7620 (tpt) REVERT: C 128 ASN cc_start: 0.8752 (t0) cc_final: 0.8521 (t0) REVERT: D 2 MET cc_start: 0.7945 (tpp) cc_final: 0.7629 (tpt) REVERT: D 128 ASN cc_start: 0.8803 (OUTLIER) cc_final: 0.8405 (t0) REVERT: D 634 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8701 (tp40) REVERT: D 819 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7801 (pm20) outliers start: 25 outliers final: 16 residues processed: 385 average time/residue: 0.8570 time to fit residues: 384.6468 Evaluate side-chains 363 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 344 time to evaluate : 1.489 ------------------------------------------------------------------------------- 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 128 ASN 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 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: 0.8980 chunk 320 optimal weight: 8.9990 chunk 333 optimal weight: 0.7980 chunk 266 optimal weight: 7.9990 chunk 398 optimal weight: 0.9990 chunk 130 optimal weight: 8.9990 chunk 212 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 chunk 381 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN A 739 HIS A 817 GLN A 863 GLN B 262 GLN B 739 HIS B 817 GLN B 863 GLN C 262 GLN C 634 GLN C 739 HIS C 817 GLN C 863 GLN D 262 GLN D 739 HIS D 817 GLN D 863 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.092711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.071403 restraints weight = 47626.075| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.78 r_work: 0.2752 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9146 moved from start: 0.1846 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= 0.139 Angle : 0.552 11.343 46156 Z= 0.286 Chirality : 0.044 0.164 4844 Planarity : 0.004 0.030 6080 Dihedral : 5.825 59.144 4576 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.83 % Allowed : 7.90 % Favored : 91.27 % 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 aren not related in a simple way. whole: 0.53 (0.13), residues: 4076 helix: 0.52 (0.23), residues: 508 sheet: 0.94 (0.14), residues: 1328 loop : 0.03 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 251 TYR 0.019 0.001 TYR B 100 PHE 0.009 0.001 PHE D 758 TRP 0.034 0.001 TRP C 553 HIS 0.006 0.001 HIS C 395 Details of bonding type rmsd covalent geometry : bond 0.00303 (33824) covalent geometry : angle 0.55154 (46156) hydrogen bonds : bond 0.03790 ( 1208) hydrogen bonds : angle 5.11109 ( 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 401 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 372 time to evaluate : 1.102 Fit side-chains REVERT: A 2 MET cc_start: 0.7973 (tpp) cc_final: 0.7649 (tpt) REVERT: A 117 GLU cc_start: 0.8204 (mp0) cc_final: 0.7854 (pm20) REVERT: A 128 ASN cc_start: 0.8714 (t0) cc_final: 0.8451 (t0) REVERT: A 136 GLU cc_start: 0.8552 (pm20) cc_final: 0.8279 (pt0) REVERT: A 965 GLN cc_start: 0.9010 (tt0) cc_final: 0.8758 (tt0) REVERT: B 2 MET cc_start: 0.7977 (tpp) cc_final: 0.7651 (tpt) REVERT: B 117 GLU cc_start: 0.8211 (mp0) cc_final: 0.7869 (pm20) REVERT: B 136 GLU cc_start: 0.8530 (pm20) cc_final: 0.8273 (pt0) REVERT: B 965 GLN cc_start: 0.9019 (tt0) cc_final: 0.8769 (tt0) REVERT: C 2 MET cc_start: 0.7976 (tpp) cc_final: 0.7650 (tpt) REVERT: C 117 GLU cc_start: 0.8198 (mp0) cc_final: 0.7847 (pm20) REVERT: C 128 ASN cc_start: 0.8716 (t0) cc_final: 0.8452 (t0) REVERT: C 136 GLU cc_start: 0.8563 (pm20) cc_final: 0.8285 (pt0) REVERT: C 819 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7762 (pm20) REVERT: C 965 GLN cc_start: 0.9000 (tt0) cc_final: 0.8758 (tt0) REVERT: D 2 MET cc_start: 0.7960 (tpp) cc_final: 0.7636 (tpt) REVERT: D 117 GLU cc_start: 0.8210 (mp0) cc_final: 0.7859 (pm20) REVERT: D 136 GLU cc_start: 0.8531 (pm20) cc_final: 0.8278 (pt0) REVERT: D 965 GLN cc_start: 0.9008 (tt0) cc_final: 0.8762 (tt0) outliers start: 29 outliers final: 16 residues processed: 386 average time/residue: 0.8094 time to fit residues: 365.0544 Evaluate side-chains 354 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 338 time to evaluate : 1.464 ------------------------------------------------------------------------------- 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: 5.9990 chunk 277 optimal weight: 0.1980 chunk 14 optimal weight: 0.9990 chunk 283 optimal weight: 7.9990 chunk 112 optimal weight: 0.0060 chunk 354 optimal weight: 7.9990 chunk 349 optimal weight: 1.9990 chunk 212 optimal weight: 0.6980 chunk 398 optimal weight: 1.9990 chunk 214 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN A 634 GLN A 739 HIS A 844 HIS ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN B 634 GLN B 739 HIS B 844 HIS C 262 GLN C 634 GLN C 739 HIS C 844 HIS ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 GLN D 739 HIS D 844 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.095731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.074423 restraints weight = 47404.545| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.79 r_work: 0.2817 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9107 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 33824 Z= 0.096 Angle : 0.511 10.613 46156 Z= 0.264 Chirality : 0.043 0.166 4844 Planarity : 0.003 0.030 6080 Dihedral : 5.513 58.991 4576 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.86 % Allowed : 8.53 % Favored : 90.61 % 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 aren not related in a simple way. whole: 0.60 (0.13), residues: 4076 helix: 0.77 (0.23), residues: 512 sheet: 0.96 (0.14), residues: 1348 loop : 0.03 (0.13), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 251 TYR 0.018 0.001 TYR C 100 PHE 0.009 0.001 PHE B 758 TRP 0.033 0.001 TRP C 553 HIS 0.004 0.001 HIS D 395 Details of bonding type rmsd covalent geometry : bond 0.00207 (33824) covalent geometry : angle 0.51125 (46156) hydrogen bonds : bond 0.03211 ( 1208) hydrogen bonds : angle 4.88146 ( 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 414 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 384 time to evaluate : 1.709 Fit side-chains REVERT: A 2 MET cc_start: 0.7980 (tpp) cc_final: 0.7645 (tpt) REVERT: A 117 GLU cc_start: 0.8223 (mp0) cc_final: 0.7871 (pm20) REVERT: A 438 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8514 (mt-10) REVERT: A 634 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8664 (tp40) REVERT: A 754 LYS cc_start: 0.9058 (mttp) cc_final: 0.8839 (mttm) REVERT: B 2 MET cc_start: 0.7992 (tpp) cc_final: 0.7654 (tpt) REVERT: B 117 GLU cc_start: 0.8237 (mp0) cc_final: 0.7886 (pm20) REVERT: B 136 GLU cc_start: 0.8567 (pm20) cc_final: 0.8335 (pm20) REVERT: B 438 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8527 (mt-10) REVERT: B 634 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8658 (tp40) REVERT: B 754 LYS cc_start: 0.9054 (mttp) cc_final: 0.8834 (mttm) REVERT: C 2 MET cc_start: 0.7994 (tpp) cc_final: 0.7658 (tpt) REVERT: C 117 GLU cc_start: 0.8228 (mp0) cc_final: 0.7877 (pm20) REVERT: C 438 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8518 (mt-10) REVERT: C 754 LYS cc_start: 0.9062 (mttp) cc_final: 0.8843 (mttm) REVERT: D 2 MET cc_start: 0.7989 (tpp) cc_final: 0.7650 (tpt) REVERT: D 117 GLU cc_start: 0.8232 (mp0) cc_final: 0.7882 (pm20) REVERT: D 136 GLU cc_start: 0.8577 (pm20) cc_final: 0.8350 (pm20) REVERT: D 438 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8532 (mt-10) REVERT: D 754 LYS cc_start: 0.9062 (mttp) cc_final: 0.8847 (mttm) outliers start: 30 outliers final: 16 residues processed: 400 average time/residue: 0.8697 time to fit residues: 405.7464 Evaluate side-chains 372 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 354 time to evaluate : 1.346 ------------------------------------------------------------------------------- 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 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 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: 5.9990 chunk 229 optimal weight: 0.9990 chunk 295 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 292 optimal weight: 0.9990 chunk 191 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 239 optimal weight: 9.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN A 634 GLN A 739 HIS A 817 GLN A 896 ASN B 262 GLN B 634 GLN B 739 HIS B 896 ASN C 262 GLN C 634 GLN C 739 HIS C 817 GLN C 896 ASN ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 GLN D 634 GLN D 739 HIS D 896 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.095449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.074139 restraints weight = 47190.211| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.79 r_work: 0.2810 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9111 moved from start: 0.2125 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= 0.107 Angle : 0.527 9.967 46156 Z= 0.271 Chirality : 0.043 0.162 4844 Planarity : 0.003 0.032 6080 Dihedral : 5.497 58.298 4576 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.80 % Allowed : 8.76 % 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 aren not related in a simple way. whole: 0.64 (0.13), residues: 4076 helix: 0.84 (0.23), residues: 512 sheet: 0.99 (0.14), residues: 1336 loop : 0.05 (0.13), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 251 TYR 0.018 0.001 TYR D 100 PHE 0.009 0.001 PHE C 225 TRP 0.029 0.001 TRP D 553 HIS 0.004 0.001 HIS A 395 Details of bonding type rmsd covalent geometry : bond 0.00236 (33824) covalent geometry : angle 0.52729 (46156) hydrogen bonds : bond 0.03332 ( 1208) hydrogen bonds : angle 4.87807 ( 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 398 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 370 time to evaluate : 1.416 Fit side-chains REVERT: A 2 MET cc_start: 0.7965 (tpp) cc_final: 0.7627 (tpt) REVERT: A 117 GLU cc_start: 0.8222 (mp0) cc_final: 0.7857 (pm20) REVERT: A 438 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8528 (mt-10) REVERT: A 754 LYS cc_start: 0.9060 (mttp) cc_final: 0.8842 (mttm) REVERT: B 2 MET cc_start: 0.7967 (tpp) cc_final: 0.7629 (tpt) REVERT: B 117 GLU cc_start: 0.8216 (mp0) cc_final: 0.7862 (pm20) REVERT: B 438 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8529 (mt-10) REVERT: B 754 LYS cc_start: 0.9062 (mttp) cc_final: 0.8847 (mttm) REVERT: C 2 MET cc_start: 0.7978 (tpp) cc_final: 0.7639 (tpt) REVERT: C 117 GLU cc_start: 0.8224 (mp0) cc_final: 0.7861 (pm20) REVERT: C 438 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8532 (mt-10) REVERT: C 754 LYS cc_start: 0.9062 (mttp) cc_final: 0.8843 (mttm) REVERT: D 2 MET cc_start: 0.7978 (tpp) cc_final: 0.7640 (tpt) REVERT: D 117 GLU cc_start: 0.8221 (mp0) cc_final: 0.7854 (pm20) REVERT: D 438 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8531 (mt-10) REVERT: D 754 LYS cc_start: 0.9063 (mttp) cc_final: 0.8850 (mttm) outliers start: 28 outliers final: 16 residues processed: 387 average time/residue: 0.8676 time to fit residues: 391.2910 Evaluate side-chains 363 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 347 time to evaluate : 1.412 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 91 optimal weight: 7.9990 chunk 336 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 221 optimal weight: 6.9990 chunk 274 optimal weight: 8.9990 chunk 194 optimal weight: 5.9990 chunk 202 optimal weight: 0.1980 chunk 131 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 345 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 634 GLN A 739 HIS ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 634 GLN B 739 HIS C 634 GLN C 739 HIS ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 634 GLN D 739 HIS ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.096744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.075623 restraints weight = 47379.717| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.78 r_work: 0.2840 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9092 moved from start: 0.2263 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= 0.094 Angle : 0.511 9.854 46156 Z= 0.263 Chirality : 0.043 0.160 4844 Planarity : 0.003 0.034 6080 Dihedral : 5.374 58.144 4576 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.80 % Allowed : 8.88 % 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 aren not related in a simple way. whole: 0.67 (0.13), residues: 4076 helix: 0.90 (0.24), residues: 512 sheet: 1.02 (0.14), residues: 1336 loop : 0.05 (0.13), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 251 TYR 0.017 0.001 TYR C 100 PHE 0.009 0.001 PHE D 225 TRP 0.030 0.001 TRP C 553 HIS 0.003 0.001 HIS D 395 Details of bonding type rmsd covalent geometry : bond 0.00208 (33824) covalent geometry : angle 0.51118 (46156) hydrogen bonds : bond 0.03107 ( 1208) hydrogen bonds : angle 4.79110 ( 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 388 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 360 time to evaluate : 1.367 Fit side-chains REVERT: A 2 MET cc_start: 0.7960 (tpp) cc_final: 0.7559 (tpt) REVERT: A 117 GLU cc_start: 0.8223 (mp0) cc_final: 0.7864 (pm20) REVERT: A 262 GLN cc_start: 0.8690 (tp40) cc_final: 0.8241 (tt0) REVERT: A 438 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8495 (mt-10) REVERT: B 2 MET cc_start: 0.7960 (tpp) cc_final: 0.7559 (tpt) REVERT: B 117 GLU cc_start: 0.8216 (mp0) cc_final: 0.7863 (pm20) REVERT: B 262 GLN cc_start: 0.8696 (tp40) cc_final: 0.8240 (tt0) REVERT: B 438 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8488 (mt-10) REVERT: B 754 LYS cc_start: 0.9037 (mttp) cc_final: 0.8836 (mttm) REVERT: C 2 MET cc_start: 0.7975 (tpp) cc_final: 0.7571 (tpt) REVERT: C 117 GLU cc_start: 0.8228 (mp0) cc_final: 0.7867 (pm20) REVERT: C 262 GLN cc_start: 0.8683 (tp40) cc_final: 0.8238 (tt0) REVERT: C 271 THR cc_start: 0.9208 (t) cc_final: 0.8958 (m) REVERT: C 438 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8465 (mt-10) REVERT: D 2 MET cc_start: 0.7967 (tpp) cc_final: 0.7564 (tpt) REVERT: D 117 GLU cc_start: 0.8231 (mp0) cc_final: 0.7866 (pm20) REVERT: D 438 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8489 (mt-10) outliers start: 28 outliers final: 20 residues processed: 383 average time/residue: 0.8276 time to fit residues: 370.1610 Evaluate side-chains 374 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 354 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 265 THR 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 265 THR 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 265 THR 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 265 THR 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: 5.9990 chunk 195 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 129 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 312 optimal weight: 2.9990 chunk 372 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 238 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 634 GLN A 739 HIS A 817 GLN B 634 GLN B 739 HIS C 739 HIS C 817 GLN D 739 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.095264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.073838 restraints weight = 47195.371| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.79 r_work: 0.2804 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9115 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 33824 Z= 0.113 Angle : 0.532 9.566 46156 Z= 0.274 Chirality : 0.043 0.160 4844 Planarity : 0.004 0.033 6080 Dihedral : 5.483 57.384 4576 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.72 % Allowed : 8.91 % Favored : 90.38 % 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 aren not related in a simple way. whole: 0.68 (0.13), residues: 4076 helix: 0.85 (0.23), residues: 512 sheet: 1.04 (0.14), residues: 1336 loop : 0.07 (0.13), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 251 TYR 0.018 0.001 TYR A 100 PHE 0.011 0.001 PHE A 225 TRP 0.027 0.001 TRP C 553 HIS 0.004 0.001 HIS B 395 Details of bonding type rmsd covalent geometry : bond 0.00250 (33824) covalent geometry : angle 0.53206 (46156) hydrogen bonds : bond 0.03367 ( 1208) hydrogen bonds : angle 4.83934 ( 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 389 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 364 time to evaluate : 1.412 Fit side-chains REVERT: A 2 MET cc_start: 0.7987 (tpp) cc_final: 0.7592 (tpt) REVERT: A 117 GLU cc_start: 0.8216 (mp0) cc_final: 0.7841 (pm20) REVERT: A 262 GLN cc_start: 0.8701 (tp40) cc_final: 0.8299 (tt0) REVERT: A 438 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8551 (mt-10) REVERT: B 2 MET cc_start: 0.7986 (tpp) cc_final: 0.7593 (tpt) REVERT: B 117 GLU cc_start: 0.8203 (mp0) cc_final: 0.7846 (pm20) REVERT: B 262 GLN cc_start: 0.8708 (tp40) cc_final: 0.8300 (tt0) REVERT: B 438 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8543 (mt-10) REVERT: B 744 GLU cc_start: 0.8057 (pm20) cc_final: 0.7840 (pm20) REVERT: B 754 LYS cc_start: 0.9050 (mttp) cc_final: 0.8835 (mttm) REVERT: C 2 MET cc_start: 0.7996 (tpp) cc_final: 0.7603 (tpt) REVERT: C 117 GLU cc_start: 0.8212 (mp0) cc_final: 0.7842 (pm20) REVERT: C 262 GLN cc_start: 0.8700 (tp40) cc_final: 0.8303 (tt0) REVERT: C 438 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8548 (mt-10) REVERT: C 744 GLU cc_start: 0.8042 (pm20) cc_final: 0.7836 (pm20) REVERT: D 2 MET cc_start: 0.7982 (tpp) cc_final: 0.7589 (tpt) REVERT: D 117 GLU cc_start: 0.8207 (mp0) cc_final: 0.7834 (pm20) REVERT: D 262 GLN cc_start: 0.8698 (tp40) cc_final: 0.8294 (tt0) REVERT: D 438 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8543 (mt-10) outliers start: 25 outliers final: 20 residues processed: 383 average time/residue: 0.9112 time to fit residues: 407.3988 Evaluate side-chains 375 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 355 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 265 THR 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 265 THR 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 265 THR 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 265 THR 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.4333 > 50: distance: 71 - 78: 11.563 distance: 78 - 79: 8.744 distance: 78 - 84: 27.802 distance: 79 - 80: 12.977 distance: 79 - 82: 32.166 distance: 80 - 81: 33.336 distance: 80 - 85: 23.254 distance: 82 - 83: 17.267 distance: 83 - 84: 52.433 distance: 85 - 86: 10.032 distance: 86 - 87: 7.636 distance: 86 - 89: 8.341 distance: 87 - 88: 18.447 distance: 87 - 96: 20.729 distance: 89 - 90: 17.033 distance: 90 - 91: 9.390 distance: 90 - 92: 8.905 distance: 91 - 93: 4.871 distance: 92 - 94: 5.959 distance: 93 - 95: 13.998 distance: 94 - 95: 12.596 distance: 96 - 97: 24.865 distance: 96 - 102: 20.480 distance: 97 - 98: 8.517 distance: 97 - 100: 10.586 distance: 98 - 99: 11.696 distance: 98 - 103: 25.606 distance: 101 - 102: 24.573 distance: 103 - 104: 15.941 distance: 104 - 105: 15.965 distance: 104 - 107: 21.562 distance: 105 - 106: 11.670 distance: 105 - 108: 20.773 distance: 108 - 109: 25.065 distance: 109 - 110: 13.948 distance: 109 - 112: 8.663 distance: 110 - 111: 13.382 distance: 110 - 115: 7.980 distance: 112 - 113: 17.119 distance: 112 - 114: 24.362 distance: 115 - 116: 10.431 distance: 115 - 121: 12.850 distance: 116 - 117: 8.647 distance: 116 - 119: 16.934 distance: 117 - 118: 7.697 distance: 117 - 122: 4.726 distance: 119 - 120: 14.740 distance: 120 - 121: 6.013 distance: 122 - 123: 7.528 distance: 123 - 124: 6.046 distance: 123 - 126: 14.883 distance: 124 - 125: 14.591 distance: 124 - 131: 10.970 distance: 126 - 127: 15.339 distance: 127 - 128: 8.220 distance: 128 - 129: 13.006 distance: 129 - 130: 13.281 distance: 131 - 132: 20.149 distance: 132 - 133: 16.190 distance: 132 - 135: 36.517 distance: 133 - 134: 11.195 distance: 133 - 145: 7.996 distance: 135 - 136: 26.601 distance: 136 - 137: 15.634 distance: 136 - 138: 13.180 distance: 137 - 139: 15.605 distance: 138 - 140: 11.633 distance: 138 - 141: 7.376 distance: 139 - 140: 6.333 distance: 140 - 142: 10.207 distance: 142 - 144: 5.979 distance: 143 - 144: 6.114 distance: 145 - 146: 6.557 distance: 146 - 147: 18.067 distance: 146 - 149: 4.233 distance: 147 - 148: 14.760 distance: 147 - 151: 20.161 distance: 148 - 174: 13.347 distance: 149 - 150: 15.027 distance: 151 - 152: 13.551 distance: 152 - 153: 10.833 distance: 152 - 155: 14.660 distance: 153 - 154: 8.125 distance: 153 - 159: 9.876 distance: 155 - 156: 8.982 distance: 155 - 157: 6.678 distance: 156 - 158: 6.592