Starting phenix.real_space_refine on Thu Aug 8 22:29:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vks_21228/08_2024/6vks_21228.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vks_21228/08_2024/6vks_21228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vks_21228/08_2024/6vks_21228.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vks_21228/08_2024/6vks_21228.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vks_21228/08_2024/6vks_21228.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vks_21228/08_2024/6vks_21228.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 137 5.16 5 C 15458 2.51 5 N 3920 2.21 5 O 4504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 336": "OE1" <-> "OE2" Residue "A PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 525": "OE1" <-> "OE2" Residue "A GLU 697": "OE1" <-> "OE2" Residue "B GLU 168": "OE1" <-> "OE2" Residue "B GLU 669": "OE1" <-> "OE2" Residue "B GLU 719": "OE1" <-> "OE2" Residue "B GLU 855": "OE1" <-> "OE2" Residue "B PHE 1039": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 24034 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1049, 7864 Classifications: {'peptide': 1049} Link IDs: {'PTRANS': 40, 'TRANS': 1008} Chain: "B" Number of atoms: 7788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 7788 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 40, 'TRANS': 999} Chain: "C" Number of atoms: 7806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 7806 Classifications: {'peptide': 1042} Link IDs: {'PTRANS': 40, 'TRANS': 1001} Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 101 Unusual residues: {'PTY': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 201 Unusual residues: {'AIX': 1, 'PTY': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'AIX:plan-4': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 274 Unusual residues: {'PTY': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PTY:plan-2': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 14.46, per 1000 atoms: 0.60 Number of scatterers: 24034 At special positions: 0 Unit cell: (123.2, 116.6, 147.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 137 16.00 P 15 15.00 O 4504 8.00 N 3920 7.00 C 15458 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 - 3.50 Amino acid : False - 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.45 Conformation dependent library (CDL) restraints added in 4.2 seconds 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5704 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 21 sheets defined 55.2% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.00 Creating SS restraints... Processing helix chain 'A' and resid 8 through 29 removed outlier: 4.088A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A 15 " --> pdb=" O PHE A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 69 removed outlier: 3.717A pdb=" N SER A 60 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N SER A 63 " --> pdb=" O GLY A 59 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N VAL A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 113 Processing helix chain 'A' and resid 114 through 118 removed outlier: 3.939A pdb=" N LEU A 118 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 removed outlier: 3.681A pdb=" N TYR A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 160 Processing helix chain 'A' and resid 160 through 165 Processing helix chain 'A' and resid 187 through 192 removed outlier: 3.682A pdb=" N LEU A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN A 192 " --> pdb=" O PRO A 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 187 through 192' Processing helix chain 'A' and resid 197 through 209 removed outlier: 3.516A pdb=" N VAL A 201 " --> pdb=" O SER A 197 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 245 Processing helix chain 'A' and resid 259 through 263 removed outlier: 4.296A pdb=" N VAL A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 259 through 263' Processing helix chain 'A' and resid 298 through 311 Processing helix chain 'A' and resid 327 through 358 removed outlier: 4.052A pdb=" N VAL A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 358 " --> pdb=" O TYR A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 365 through 384 Proline residue: A 371 - end of helix Processing helix chain 'A' and resid 389 through 422 removed outlier: 3.620A pdb=" N MET A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL A 414 " --> pdb=" O VAL A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 452 removed outlier: 5.607A pdb=" N GLY A 438 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ALA A 439 " --> pdb=" O GLN A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 456 removed outlier: 3.805A pdb=" N MET A 456 " --> pdb=" O PRO A 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 453 through 456' Processing helix chain 'A' and resid 461 through 494 removed outlier: 3.543A pdb=" N TYR A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLN A 467 " --> pdb=" O ASN A 463 " (cutoff:3.500A) Proline residue: A 488 - end of helix removed outlier: 3.558A pdb=" N MET A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 533 removed outlier: 4.185A pdb=" N ALA A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS A 530 " --> pdb=" O GLY A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 554 removed outlier: 3.575A pdb=" N VAL A 540 " --> pdb=" O PHE A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 596 removed outlier: 3.848A pdb=" N THR A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 586 " --> pdb=" O GLU A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 653 removed outlier: 3.618A pdb=" N GLY A 644 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 671 removed outlier: 3.570A pdb=" N LEU A 670 " --> pdb=" O ILE A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 704 Processing helix chain 'A' and resid 729 through 734 Processing helix chain 'A' and resid 740 through 751 removed outlier: 4.337A pdb=" N LEU A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 847 removed outlier: 3.534A pdb=" N ALA A 837 " --> pdb=" O SER A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 864 removed outlier: 4.156A pdb=" N GLU A 862 " --> pdb=" O GLY A 858 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU A 863 " --> pdb=" O GLN A 859 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 864 " --> pdb=" O SER A 860 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 858 through 864' Processing helix chain 'A' and resid 869 through 890 removed outlier: 4.135A pdb=" N ALA A 875 " --> pdb=" O ILE A 871 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU A 876 " --> pdb=" O ALA A 872 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 877 " --> pdb=" O LEU A 873 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 878 " --> pdb=" O TYR A 874 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 879 " --> pdb=" O ALA A 875 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 884 " --> pdb=" O ALA A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 899 removed outlier: 4.002A pdb=" N ALA A 897 " --> pdb=" O SER A 893 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 898 " --> pdb=" O ILE A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 920 removed outlier: 4.276A pdb=" N LEU A 906 " --> pdb=" O MET A 902 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU A 918 " --> pdb=" O THR A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 958 removed outlier: 3.864A pdb=" N GLN A 936 " --> pdb=" O ASP A 932 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A 937 " --> pdb=" O ILE A 933 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLY A 938 " --> pdb=" O TYR A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 990 removed outlier: 3.532A pdb=" N LEU A 972 " --> pdb=" O VAL A 968 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ARG A 980 " --> pdb=" O ARG A 976 " (cutoff:3.500A) Proline residue: A 981 - end of helix Processing helix chain 'A' and resid 993 through 999 Processing helix chain 'A' and resid 1004 through 1041 removed outlier: 4.060A pdb=" N THR A1022 " --> pdb=" O MET A1018 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A1023 " --> pdb=" O LEU A1019 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A1026 " --> pdb=" O THR A1022 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N PHE A1027 " --> pdb=" O LEU A1023 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A1029 " --> pdb=" O SER A1025 " (cutoff:3.500A) Proline residue: A1030 - end of helix Processing helix chain 'B' and resid 8 through 28 removed outlier: 3.699A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE B 15 " --> pdb=" O PHE B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 67 removed outlier: 5.427A pdb=" N SER B 63 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N VAL B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG B 67 " --> pdb=" O SER B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 115 removed outlier: 3.964A pdb=" N GLU B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 119 through 126 removed outlier: 3.661A pdb=" N GLN B 123 " --> pdb=" O PRO B 119 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR B 125 " --> pdb=" O THR B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 160 removed outlier: 3.549A pdb=" N MET B 152 " --> pdb=" O SER B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 165 removed outlier: 3.547A pdb=" N GLN B 165 " --> pdb=" O VAL B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 194 removed outlier: 3.551A pdb=" N LEU B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 208 Processing helix chain 'B' and resid 240 through 245 Processing helix chain 'B' and resid 297 through 313 removed outlier: 3.571A pdb=" N LYS B 302 " --> pdb=" O MET B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 357 removed outlier: 4.039A pdb=" N GLU B 332 " --> pdb=" O SER B 328 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE B 333 " --> pdb=" O LYS B 329 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER B 334 " --> pdb=" O PHE B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 384 removed outlier: 4.227A pdb=" N THR B 367 " --> pdb=" O THR B 363 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE B 368 " --> pdb=" O LEU B 364 " (cutoff:3.500A) Proline residue: B 371 - end of helix Processing helix chain 'B' and resid 389 through 399 Processing helix chain 'B' and resid 399 through 421 removed outlier: 3.790A pdb=" N ASP B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA B 407 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN B 413 " --> pdb=" O VAL B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 452 removed outlier: 5.711A pdb=" N GLY B 438 " --> pdb=" O GLY B 434 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ALA B 439 " --> pdb=" O GLN B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 457 removed outlier: 3.579A pdb=" N MET B 456 " --> pdb=" O PRO B 453 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE B 457 " --> pdb=" O LEU B 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 453 through 457' Processing helix chain 'B' and resid 459 through 494 removed outlier: 4.138A pdb=" N GLN B 467 " --> pdb=" O ASN B 463 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE B 468 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N THR B 487 " --> pdb=" O ALA B 483 " (cutoff:3.500A) Proline residue: B 488 - end of helix Processing helix chain 'B' and resid 508 through 532 removed outlier: 4.250A pdb=" N TRP B 512 " --> pdb=" O GLY B 508 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE B 513 " --> pdb=" O PHE B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 555 removed outlier: 3.549A pdb=" N MET B 538 " --> pdb=" O LYS B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 596 removed outlier: 3.732A pdb=" N THR B 584 " --> pdb=" O THR B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 654 removed outlier: 3.519A pdb=" N GLY B 652 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 704 Processing helix chain 'B' and resid 729 through 735 Processing helix chain 'B' and resid 740 through 751 removed outlier: 3.572A pdb=" N ARG B 744 " --> pdb=" O PHE B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 847 removed outlier: 3.780A pdb=" N ALA B 837 " --> pdb=" O SER B 833 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU B 839 " --> pdb=" O GLY B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 864 removed outlier: 3.681A pdb=" N GLU B 863 " --> pdb=" O GLN B 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 890 Processing helix chain 'B' and resid 893 through 899 Processing helix chain 'B' and resid 901 through 923 removed outlier: 3.864A pdb=" N GLY B 905 " --> pdb=" O VAL B 901 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU B 906 " --> pdb=" O MET B 902 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU B 922 " --> pdb=" O LEU B 918 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 923 " --> pdb=" O PHE B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 959 removed outlier: 3.666A pdb=" N ASP B 959 " --> pdb=" O GLU B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 998 removed outlier: 5.179A pdb=" N ARG B 980 " --> pdb=" O ARG B 976 " (cutoff:3.500A) Proline residue: B 981 - end of helix Proline residue: B 995 - end of helix removed outlier: 3.527A pdb=" N ILE B 998 " --> pdb=" O VAL B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1040 removed outlier: 3.750A pdb=" N GLN B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR B1013 " --> pdb=" O ALA B1009 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N PHE B1027 " --> pdb=" O LEU B1023 " (cutoff:3.500A) Proline residue: B1030 - end of helix Processing helix chain 'C' and resid 3 through 8 removed outlier: 4.280A pdb=" N ASP C 7 " --> pdb=" O LYS C 3 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG C 8 " --> pdb=" O PHE C 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3 through 8' Processing helix chain 'C' and resid 8 through 28 removed outlier: 3.932A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 61 through 69 removed outlier: 3.677A pdb=" N ILE C 65 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 112 removed outlier: 4.002A pdb=" N ALA C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL C 105 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN C 108 " --> pdb=" O GLN C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'C' and resid 121 through 126 removed outlier: 3.633A pdb=" N TYR C 125 " --> pdb=" O THR C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 159 removed outlier: 3.834A pdb=" N MET C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 166 removed outlier: 3.665A pdb=" N GLU C 163 " --> pdb=" O ASN C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 removed outlier: 3.566A pdb=" N LEU C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 208 Processing helix chain 'C' and resid 240 through 245 removed outlier: 3.552A pdb=" N GLY C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 312 removed outlier: 3.631A pdb=" N LYS C 302 " --> pdb=" O MET C 298 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA C 303 " --> pdb=" O ALA C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 315 No H-bonds generated for 'chain 'C' and resid 313 through 315' Processing helix chain 'C' and resid 330 through 358 removed outlier: 3.989A pdb=" N GLU C 336 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL C 349 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE C 350 " --> pdb=" O MET C 346 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 352 " --> pdb=" O LEU C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 384 removed outlier: 3.936A pdb=" N THR C 363 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU C 364 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE C 365 " --> pdb=" O ARG C 361 " (cutoff:3.500A) Proline residue: C 366 - end of helix removed outlier: 4.144A pdb=" N VAL C 369 " --> pdb=" O ILE C 365 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL C 370 " --> pdb=" O PRO C 366 " (cutoff:3.500A) Proline residue: C 371 - end of helix removed outlier: 3.553A pdb=" N MET C 384 " --> pdb=" O PHE C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 401 removed outlier: 3.519A pdb=" N MET C 393 " --> pdb=" O ASN C 389 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY C 401 " --> pdb=" O ILE C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 416 removed outlier: 3.566A pdb=" N GLU C 412 " --> pdb=" O ILE C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 424 through 436 removed outlier: 3.516A pdb=" N THR C 429 " --> pdb=" O PRO C 425 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 449 removed outlier: 3.643A pdb=" N GLY C 442 " --> pdb=" O GLY C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 456 removed outlier: 3.593A pdb=" N MET C 456 " --> pdb=" O PRO C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 494 removed outlier: 4.037A pdb=" N THR C 471 " --> pdb=" O GLN C 467 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR C 487 " --> pdb=" O ALA C 483 " (cutoff:3.500A) Proline residue: C 488 - end of helix Processing helix chain 'C' and resid 508 through 532 removed outlier: 3.582A pdb=" N TRP C 512 " --> pdb=" O GLY C 508 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY C 526 " --> pdb=" O HIS C 522 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA C 529 " --> pdb=" O GLU C 525 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS C 530 " --> pdb=" O GLY C 526 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL C 531 " --> pdb=" O ARG C 527 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 532 " --> pdb=" O VAL C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 555 removed outlier: 3.562A pdb=" N ARG C 555 " --> pdb=" O PHE C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 596 removed outlier: 3.760A pdb=" N THR C 584 " --> pdb=" O THR C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 654 removed outlier: 3.515A pdb=" N LYS C 645 " --> pdb=" O ALA C 641 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR C 647 " --> pdb=" O ALA C 643 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY C 648 " --> pdb=" O GLY C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 703 Processing helix chain 'C' and resid 729 through 737 Processing helix chain 'C' and resid 739 through 750 removed outlier: 4.195A pdb=" N ILE C 743 " --> pdb=" O SER C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 780 through 785 removed outlier: 3.542A pdb=" N LEU C 784 " --> pdb=" O PRO C 780 " (cutoff:3.500A) Processing helix chain 'C' and resid 797 through 801 removed outlier: 4.158A pdb=" N ILE C 801 " --> pdb=" O PRO C 797 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 797 through 801' Processing helix chain 'C' and resid 833 through 846 removed outlier: 3.850A pdb=" N ALA C 837 " --> pdb=" O SER C 833 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASP C 846 " --> pdb=" O GLN C 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 866 removed outlier: 3.696A pdb=" N GLU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 889 removed outlier: 3.813A pdb=" N ALA C 872 " --> pdb=" O SER C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 899 removed outlier: 3.876A pdb=" N ALA C 897 " --> pdb=" O SER C 893 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL C 898 " --> pdb=" O ILE C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 924 Processing helix chain 'C' and resid 932 through 962 removed outlier: 3.926A pdb=" N ILE C 953 " --> pdb=" O ASN C 949 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N PHE C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP C 959 " --> pdb=" O GLU C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 998 removed outlier: 3.845A pdb=" N GLU C 973 " --> pdb=" O GLU C 969 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ARG C 980 " --> pdb=" O ARG C 976 " (cutoff:3.500A) Proline residue: C 981 - end of helix removed outlier: 3.724A pdb=" N ALA C 988 " --> pdb=" O MET C 984 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE C 989 " --> pdb=" O THR C 985 " (cutoff:3.500A) Proline residue: C 995 - end of helix Processing helix chain 'C' and resid 1004 through 1040 removed outlier: 3.930A pdb=" N ARG C1008 " --> pdb=" O SER C1004 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR C1013 " --> pdb=" O ALA C1009 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE C1027 " --> pdb=" O LEU C1023 " (cutoff:3.500A) Proline residue: C1030 - end of helix removed outlier: 4.013A pdb=" N VAL C1034 " --> pdb=" O PRO C1030 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 130 removed outlier: 4.921A pdb=" N SER A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP A 83 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 175 removed outlier: 6.947A pdb=" N VAL A 170 " --> pdb=" O SER A 292 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N SER A 292 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN A 172 " --> pdb=" O MET A 290 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET A 287 " --> pdb=" O VAL A 140 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 140 " --> pdb=" O MET A 287 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET A 138 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU A 291 " --> pdb=" O PHE A 136 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N PHE A 136 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N LEU A 137 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ASP A 326 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE A 139 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A 322 " --> pdb=" O MET A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 264 through 270 removed outlier: 8.390A pdb=" N ARG A 180 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ARG A 767 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER A 757 " --> pdb=" O VAL A 768 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL A 770 " --> pdb=" O TYR A 755 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR A 755 " --> pdb=" O VAL A 770 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 215 through 217 removed outlier: 4.014A pdb=" N GLY A 215 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 282 through 284 removed outlier: 3.673A pdb=" N VAL A 282 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR A 277 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A 276 " --> pdb=" O SER A 608 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N MET A 619 " --> pdb=" O GLY A 609 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET A 570 " --> pdb=" O VAL A 662 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 662 " --> pdb=" O MET A 570 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 676 through 680 removed outlier: 4.249A pdb=" N LEU A 676 " --> pdb=" O GLY A 826 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY A 826 " --> pdb=" O LEU A 676 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 805 through 809 removed outlier: 5.014A pdb=" N THR C 231 " --> pdb=" O PRO A 722 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY C 215 " --> pdb=" O VAL C 232 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 47 through 48 Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 48 removed outlier: 5.160A pdb=" N SER B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASP B 83 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 170 through 175 removed outlier: 6.972A pdb=" N MET B 290 " --> pdb=" O GLY B 171 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL B 173 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA B 288 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET B 287 " --> pdb=" O VAL B 140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 264 through 269 removed outlier: 3.838A pdb=" N ARG B 764 " --> pdb=" O ASN B 761 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER B 757 " --> pdb=" O VAL B 768 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL B 770 " --> pdb=" O TYR B 755 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N TYR B 755 " --> pdb=" O VAL B 770 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 216 through 217 removed outlier: 6.404A pdb=" N THR B 231 " --> pdb=" O LEU C 724 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE C 726 " --> pdb=" O THR B 231 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR B 233 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE C 728 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER C 721 " --> pdb=" O GLY C 809 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY C 809 " --> pdb=" O SER C 721 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 282 through 283 removed outlier: 3.545A pdb=" N VAL B 282 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET B 570 " --> pdb=" O VAL B 662 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 681 through 682 Processing sheet with id=AB6, first strand: chain 'B' and resid 721 through 723 Processing sheet with id=AB7, first strand: chain 'C' and resid 128 through 130 removed outlier: 4.772A pdb=" N SER C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP C 83 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR C 77 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 11.452A pdb=" N GLN C 812 " --> pdb=" O GLU C 823 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N GLU C 823 " --> pdb=" O GLN C 812 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL C 814 " --> pdb=" O ALA C 821 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 128 through 130 removed outlier: 4.772A pdb=" N SER C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP C 83 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR C 77 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 11.452A pdb=" N GLN C 812 " --> pdb=" O GLU C 823 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N GLU C 823 " --> pdb=" O GLN C 812 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL C 814 " --> pdb=" O ALA C 821 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 170 through 173 removed outlier: 7.154A pdb=" N MET C 290 " --> pdb=" O GLY C 171 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL C 173 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA C 288 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET C 138 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE C 139 " --> pdb=" O PRO C 324 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 264 through 270 removed outlier: 7.764A pdb=" N ARG C 180 " --> pdb=" O ARG C 767 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N MET C 769 " --> pdb=" O ARG C 180 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N MET C 182 " --> pdb=" O MET C 769 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N GLN C 771 " --> pdb=" O MET C 182 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ILE C 184 " --> pdb=" O GLN C 771 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER C 757 " --> pdb=" O VAL C 768 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL C 770 " --> pdb=" O TYR C 755 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N TYR C 755 " --> pdb=" O VAL C 770 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 250 through 251 removed outlier: 3.825A pdb=" N ARG C 250 " --> pdb=" O ILE C 258 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 282 through 283 removed outlier: 3.704A pdb=" N VAL C 282 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE C 623 " --> pdb=" O ILE C 605 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL C 573 " --> pdb=" O ALA C 620 " (cutoff:3.500A) 1332 hydrogen bonds defined for protein. 3891 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: 9.19 Time building geometry restraints manager: 10.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3888 1.31 - 1.44: 6083 1.44 - 1.56: 14173 1.56 - 1.69: 32 1.69 - 1.81: 270 Bond restraints: 24446 Sorted by residual: bond pdb=" C6 AIX B1106 " pdb=" S1 AIX B1106 " ideal model delta sigma weight residual 1.851 1.474 0.377 2.00e-02 2.50e+03 3.56e+02 bond pdb=" C8 PTY C1108 " pdb=" O10 PTY C1108 " ideal model delta sigma weight residual 1.205 1.451 -0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C13 AIX B1106 " pdb=" N3 AIX B1106 " ideal model delta sigma weight residual 1.447 1.667 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C13 AIX B1106 " pdb=" S1 AIX B1106 " ideal model delta sigma weight residual 1.855 1.654 0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C12 AIX B1106 " pdb=" C6 AIX B1106 " ideal model delta sigma weight residual 1.560 1.706 -0.146 2.00e-02 2.50e+03 5.36e+01 ... (remaining 24441 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.49: 688 106.49 - 113.52: 13631 113.52 - 120.55: 9903 120.55 - 127.58: 8670 127.58 - 134.61: 155 Bond angle restraints: 33047 Sorted by residual: angle pdb=" O11 PTY B1104 " pdb=" P1 PTY B1104 " pdb=" O14 PTY B1104 " ideal model delta sigma weight residual 92.90 107.55 -14.65 3.00e+00 1.11e-01 2.38e+01 angle pdb=" C13 AIX B1106 " pdb=" S1 AIX B1106 " pdb=" C6 AIX B1106 " ideal model delta sigma weight residual 93.36 106.69 -13.33 3.00e+00 1.11e-01 1.97e+01 angle pdb=" O11 PTY B1101 " pdb=" P1 PTY B1101 " pdb=" O14 PTY B1101 " ideal model delta sigma weight residual 92.90 105.87 -12.97 3.00e+00 1.11e-01 1.87e+01 angle pdb=" O11 PTY B1103 " pdb=" P1 PTY B1103 " pdb=" O14 PTY B1103 " ideal model delta sigma weight residual 92.90 105.63 -12.73 3.00e+00 1.11e-01 1.80e+01 angle pdb=" O11 PTY A1103 " pdb=" P1 PTY A1103 " pdb=" O14 PTY A1103 " ideal model delta sigma weight residual 92.90 105.58 -12.68 3.00e+00 1.11e-01 1.79e+01 ... (remaining 33042 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.27: 14399 35.27 - 70.55: 264 70.55 - 105.82: 40 105.82 - 141.09: 8 141.09 - 176.36: 7 Dihedral angle restraints: 14718 sinusoidal: 5814 harmonic: 8904 Sorted by residual: dihedral pdb=" C3 PTY B1103 " pdb=" O11 PTY B1103 " pdb=" P1 PTY B1103 " pdb=" O12 PTY B1103 " ideal model delta sinusoidal sigma weight residual -59.77 116.59 -176.36 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 PTY B1105 " pdb=" O11 PTY B1105 " pdb=" P1 PTY B1105 " pdb=" O12 PTY B1105 " ideal model delta sinusoidal sigma weight residual 300.23 124.45 175.78 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" N1 PTY B1101 " pdb=" C2 PTY B1101 " pdb=" C3 PTY B1101 " pdb=" O11 PTY B1101 " ideal model delta sinusoidal sigma weight residual 65.33 -128.71 -165.96 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 14715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3156 0.058 - 0.117: 592 0.117 - 0.175: 81 0.175 - 0.234: 16 0.234 - 0.292: 6 Chirality restraints: 3851 Sorted by residual: chirality pdb=" CA ASP C 97 " pdb=" N ASP C 97 " pdb=" C ASP C 97 " pdb=" CB ASP C 97 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA LEU B 707 " pdb=" N LEU B 707 " pdb=" C LEU B 707 " pdb=" CB LEU B 707 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA LYS B 507 " pdb=" N LYS B 507 " pdb=" C LYS B 507 " pdb=" CB LYS B 507 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 3848 not shown) Planarity restraints: 4158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 902 " 0.069 5.00e-02 4.00e+02 1.08e-01 1.85e+01 pdb=" N PRO A 903 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO A 903 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 903 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1046 " -0.020 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C GLU A1046 " 0.073 2.00e-02 2.50e+03 pdb=" O GLU A1046 " -0.028 2.00e-02 2.50e+03 pdb=" N HIS A1047 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 861 " -0.268 9.50e-02 1.11e+02 1.20e-01 8.86e+00 pdb=" NE ARG B 861 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 861 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 861 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 861 " -0.010 2.00e-02 2.50e+03 ... (remaining 4155 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 133 2.54 - 3.13: 16649 3.13 - 3.72: 35583 3.72 - 4.31: 49514 4.31 - 4.90: 84328 Nonbonded interactions: 186207 Sorted by model distance: nonbonded pdb=" O10 PTY A1103 " pdb=" O10 PTY C1104 " model vdw 1.946 3.040 nonbonded pdb=" O12 PTY C1102 " pdb=" O10 PTY C1107 " model vdw 2.053 3.040 nonbonded pdb=" NE2 GLN A 358 " pdb=" CE LYS A 507 " model vdw 2.065 3.520 nonbonded pdb=" OE1 GLN C 961 " pdb=" OH TYR C1033 " model vdw 2.188 3.040 nonbonded pdb=" NE2 GLN A 358 " pdb=" CD LYS A 507 " model vdw 2.232 3.520 ... (remaining 186202 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 1040 or (resid 1101 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C3 or name C30 or name C31 or name C32 or name C \ 33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C5 or nam \ e C6 or name C8 or name N1 or name O10 or name O11 or name O12 or name O13 or na \ me O14 or name O30 or name O4 or name O7 or name P1 )))) selection = (chain 'B' and (resid 1 through 1040 or (resid 1104 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C3 or name C30 or name C31 or name C32 or name C \ 33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C5 or nam \ e C6 or name C8 or name N1 or name O10 or name O11 or name O12 or name O13 or na \ me O14 or name O30 or name O4 or name O7 or name P1 )))) selection = (chain 'C' and (resid 1 through 1040 or resid 1107)) } 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: 1.890 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: 0.960 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 67.820 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.090 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 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 : 0.007 0.377 24446 Z= 0.458 Angle : 0.894 14.651 33047 Z= 0.462 Chirality : 0.048 0.292 3851 Planarity : 0.008 0.120 4158 Dihedral : 15.551 176.364 9014 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.11), residues: 3125 helix: -2.47 (0.09), residues: 1532 sheet: -1.98 (0.24), residues: 402 loop : -2.69 (0.14), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1016 HIS 0.008 0.001 HIS A 340 PHE 0.016 0.001 PHE B 18 TYR 0.010 0.001 TYR B 77 ARG 0.004 0.000 ARG B 744 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 543 time to evaluate : 2.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 ILE cc_start: 0.7386 (mt) cc_final: 0.7047 (mt) REVERT: A 943 MET cc_start: 0.7015 (ptm) cc_final: 0.6421 (ptt) REVERT: B 66 GLU cc_start: 0.6914 (tt0) cc_final: 0.6612 (tt0) REVERT: B 554 MET cc_start: 0.6375 (tpp) cc_final: 0.6150 (tpp) REVERT: B 1010 ILE cc_start: 0.7545 (pt) cc_final: 0.7318 (pt) REVERT: C 838 MET cc_start: 0.8583 (mtm) cc_final: 0.8350 (mtt) REVERT: C 1023 LEU cc_start: 0.7446 (mt) cc_final: 0.7208 (mt) outliers start: 0 outliers final: 0 residues processed: 543 average time/residue: 0.3633 time to fit residues: 308.2478 Evaluate side-chains 348 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 348 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.5584 > 50: distance: 1 - 15: 4.843 distance: 5 - 22: 19.937 distance: 9 - 33: 23.764 distance: 13 - 15: 3.405 distance: 14 - 41: 12.984 distance: 15 - 16: 6.473 distance: 16 - 17: 12.343 distance: 16 - 19: 7.374 distance: 17 - 18: 27.858 distance: 17 - 22: 11.752 distance: 18 - 52: 16.926 distance: 19 - 20: 11.812 distance: 19 - 21: 11.611 distance: 22 - 23: 8.526 distance: 23 - 24: 10.735 distance: 23 - 26: 11.058 distance: 24 - 25: 20.431 distance: 24 - 33: 23.565 distance: 25 - 60: 10.933 distance: 26 - 27: 3.092 distance: 27 - 28: 6.247 distance: 27 - 29: 4.918 distance: 28 - 30: 8.972 distance: 29 - 31: 6.535 distance: 30 - 32: 3.814 distance: 31 - 32: 7.914 distance: 33 - 34: 17.162 distance: 34 - 35: 15.481 distance: 34 - 37: 16.600 distance: 35 - 36: 20.166 distance: 35 - 41: 4.569 distance: 37 - 38: 4.873 distance: 38 - 39: 4.491 distance: 41 - 42: 7.035 distance: 42 - 43: 26.087 distance: 42 - 45: 29.574 distance: 43 - 44: 12.392 distance: 43 - 52: 10.608 distance: 45 - 46: 4.164 distance: 46 - 47: 9.230 distance: 46 - 48: 6.087 distance: 47 - 49: 11.703 distance: 48 - 50: 11.012 distance: 49 - 51: 9.949 distance: 50 - 51: 10.408 distance: 52 - 53: 9.245 distance: 53 - 54: 23.387 distance: 53 - 56: 13.841 distance: 54 - 55: 24.674 distance: 54 - 60: 11.811 distance: 56 - 57: 11.661 distance: 57 - 58: 13.904 distance: 58 - 59: 15.927 distance: 60 - 61: 6.281 distance: 61 - 62: 21.448 distance: 61 - 64: 22.061 distance: 62 - 63: 30.582 distance: 62 - 71: 41.020 distance: 64 - 65: 13.344 distance: 65 - 66: 14.103 distance: 66 - 67: 6.506 distance: 67 - 68: 9.207 distance: 68 - 69: 4.924 distance: 68 - 70: 6.650 distance: 71 - 72: 52.820 distance: 72 - 73: 23.895 distance: 72 - 75: 39.793 distance: 73 - 74: 21.688 distance: 73 - 79: 26.952 distance: 75 - 76: 34.087 distance: 76 - 77: 18.996 distance: 76 - 78: 33.380 distance: 79 - 80: 40.617 distance: 79 - 85: 17.463 distance: 80 - 81: 44.074 distance: 80 - 83: 15.585 distance: 81 - 82: 22.461 distance: 81 - 86: 13.626 distance: 83 - 84: 23.673 distance: 84 - 85: 46.622 distance: 86 - 87: 5.683 distance: 87 - 88: 19.317 distance: 87 - 90: 14.423 distance: 88 - 89: 48.095 distance: 88 - 93: 15.998 distance: 90 - 91: 4.601 distance: 90 - 92: 3.574 distance: 93 - 94: 21.063 distance: 94 - 95: 5.230 distance: 94 - 97: 20.305 distance: 95 - 96: 25.706 distance: 95 - 99: 20.663 distance: 97 - 98: 3.217