Starting phenix.real_space_refine on Sun Jul 5 14:01:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dic_46903/07_2026/9dic_46903.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dic_46903/07_2026/9dic_46903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dic_46903/07_2026/9dic_46903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dic_46903/07_2026/9dic_46903.map" model { file = "/net/cci-nas-00/data/ceres_data/9dic_46903/07_2026/9dic_46903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dic_46903/07_2026/9dic_46903.cif" } resolution = 2.8 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= 0.001 sd= 0.004 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 K 5 8.98 5 S 180 5.16 5 C 18444 2.51 5 N 4640 2.21 5 O 5164 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 149 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28433 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7107 Classifications: {'peptide': 905} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 36, 'TRANS': 868} Chain breaks: 5 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 80 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 5, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 7107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7107 Classifications: {'peptide': 905} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 36, 'TRANS': 868} Chain breaks: 5 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 80 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 5, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 59 Chain: "C" Number of atoms: 7107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7107 Classifications: {'peptide': 905} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 36, 'TRANS': 868} Chain breaks: 5 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 80 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 5, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 59 Chain: "D" Number of atoms: 7107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7107 Classifications: {'peptide': 905} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 36, 'TRANS': 868} Chain breaks: 5 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 80 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 5, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' K': 4} Chain breaks: 4 Time building chain proxies: 5.90, per 1000 atoms: 0.21 Number of scatterers: 28433 At special positions: 0 Unit cell: (143.505, 143.505, 129.686, 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) K 5 19.00 S 180 16.00 O 5164 8.00 N 4640 7.00 C 18444 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: 2.27 Conformation dependent library (CDL) restraints added in 1.3 seconds 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6824 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 24 sheets defined 58.0% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 15 through 44 removed outlier: 3.834A pdb=" N PHE A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 23 " --> pdb=" O PHE A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 93 Processing helix chain 'A' and resid 96 through 122 Processing helix chain 'A' and resid 136 through 160 Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 169 through 188 Proline residue: A 180 - end of helix removed outlier: 3.664A pdb=" N ILE A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 204 removed outlier: 4.050A pdb=" N PHE A 197 " --> pdb=" O GLY A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 218 through 249 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 262 through 275 Processing helix chain 'A' and resid 286 through 317 removed outlier: 3.682A pdb=" N ILE A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N GLY A 302 " --> pdb=" O MET A 298 " (cutoff:3.500A) Proline residue: A 309 - end of helix Processing helix chain 'A' and resid 341 through 353 removed outlier: 3.657A pdb=" N ASP A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 383 Processing helix chain 'A' and resid 396 through 403 Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 421 through 440 Processing helix chain 'A' and resid 453 through 460 removed outlier: 4.301A pdb=" N TYR A 457 " --> pdb=" O HIS A 453 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 458 " --> pdb=" O ASN A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 475 through 489 removed outlier: 3.516A pdb=" N LEU A 488 " --> pdb=" O ALA A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 500 removed outlier: 3.905A pdb=" N LEU A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE A 500 " --> pdb=" O MET A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 523 Processing helix chain 'A' and resid 532 through 536 Processing helix chain 'A' and resid 539 through 550 Processing helix chain 'A' and resid 592 through 602 removed outlier: 3.629A pdb=" N VAL A 596 " --> pdb=" O SER A 592 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALA A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE A 600 " --> pdb=" O VAL A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 607 removed outlier: 3.615A pdb=" N CYS A 606 " --> pdb=" O CYS A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 616 removed outlier: 3.893A pdb=" N ILE A 616 " --> pdb=" O VAL A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 725 Processing helix chain 'A' and resid 728 through 735 Processing helix chain 'A' and resid 756 through 761 Processing helix chain 'A' and resid 762 through 765 removed outlier: 4.068A pdb=" N ALA A 765 " --> pdb=" O PRO A 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 762 through 765' Processing helix chain 'A' and resid 769 through 773 Processing helix chain 'A' and resid 781 through 793 removed outlier: 3.579A pdb=" N ARG A 787 " --> pdb=" O ASP A 783 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS A 790 " --> pdb=" O HIS A 786 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N THR A 791 " --> pdb=" O ARG A 787 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 792 " --> pdb=" O GLU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 814 removed outlier: 3.535A pdb=" N LEU A 811 " --> pdb=" O ASN A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 819 removed outlier: 3.623A pdb=" N CYS A 819 " --> pdb=" O ILE A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 851 Processing helix chain 'A' and resid 882 through 886 Processing helix chain 'A' and resid 894 through 901 Processing helix chain 'A' and resid 912 through 915 Processing helix chain 'A' and resid 916 through 921 Processing helix chain 'A' and resid 928 through 931 Processing helix chain 'A' and resid 932 through 940 Processing helix chain 'A' and resid 940 through 952 removed outlier: 3.621A pdb=" N LEU A 944 " --> pdb=" O ASN A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 965 Processing helix chain 'A' and resid 975 through 980 Processing helix chain 'A' and resid 981 through 983 No H-bonds generated for 'chain 'A' and resid 981 through 983' Processing helix chain 'A' and resid 997 through 1002 removed outlier: 3.575A pdb=" N GLY A1001 " --> pdb=" O LEU A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1018 Processing helix chain 'B' and resid 15 through 44 removed outlier: 3.737A pdb=" N PHE B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER B 23 " --> pdb=" O PHE B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 93 Processing helix chain 'B' and resid 96 through 122 Processing helix chain 'B' and resid 136 through 160 Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 169 through 188 Proline residue: B 180 - end of helix removed outlier: 3.664A pdb=" N ILE B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 204 removed outlier: 4.050A pdb=" N PHE B 197 " --> pdb=" O GLY B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 218 through 249 Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 262 through 275 Processing helix chain 'B' and resid 286 through 317 removed outlier: 3.682A pdb=" N ILE B 301 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N GLY B 302 " --> pdb=" O MET B 298 " (cutoff:3.500A) Proline residue: B 309 - end of helix Processing helix chain 'B' and resid 341 through 353 removed outlier: 3.657A pdb=" N ASP B 351 " --> pdb=" O ASN B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 383 Processing helix chain 'B' and resid 396 through 403 Processing helix chain 'B' and resid 404 through 408 Processing helix chain 'B' and resid 421 through 440 Processing helix chain 'B' and resid 453 through 460 removed outlier: 4.301A pdb=" N TYR B 457 " --> pdb=" O HIS B 453 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 458 " --> pdb=" O ASN B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.516A pdb=" N LEU B 488 " --> pdb=" O ALA B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 500 removed outlier: 3.906A pdb=" N LEU B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE B 500 " --> pdb=" O MET B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 523 Processing helix chain 'B' and resid 532 through 536 Processing helix chain 'B' and resid 539 through 550 Processing helix chain 'B' and resid 592 through 602 removed outlier: 3.629A pdb=" N VAL B 596 " --> pdb=" O SER B 592 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG B 598 " --> pdb=" O GLU B 594 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALA B 599 " --> pdb=" O GLU B 595 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE B 600 " --> pdb=" O VAL B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 607 removed outlier: 3.614A pdb=" N CYS B 606 " --> pdb=" O CYS B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 616 removed outlier: 3.893A pdb=" N ILE B 616 " --> pdb=" O VAL B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 725 Processing helix chain 'B' and resid 728 through 735 Processing helix chain 'B' and resid 756 through 761 Processing helix chain 'B' and resid 762 through 765 removed outlier: 4.068A pdb=" N ALA B 765 " --> pdb=" O PRO B 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 762 through 765' Processing helix chain 'B' and resid 769 through 773 Processing helix chain 'B' and resid 781 through 793 removed outlier: 3.579A pdb=" N ARG B 787 " --> pdb=" O ASP B 783 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS B 790 " --> pdb=" O HIS B 786 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N THR B 791 " --> pdb=" O ARG B 787 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B 792 " --> pdb=" O GLU B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 814 removed outlier: 3.535A pdb=" N LEU B 811 " --> pdb=" O ASN B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 819 removed outlier: 3.623A pdb=" N CYS B 819 " --> pdb=" O ILE B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 851 Processing helix chain 'B' and resid 882 through 886 Processing helix chain 'B' and resid 894 through 901 Processing helix chain 'B' and resid 912 through 915 Processing helix chain 'B' and resid 916 through 921 Processing helix chain 'B' and resid 928 through 931 Processing helix chain 'B' and resid 932 through 940 Processing helix chain 'B' and resid 940 through 952 removed outlier: 3.620A pdb=" N LEU B 944 " --> pdb=" O ASN B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 965 Processing helix chain 'B' and resid 975 through 980 Processing helix chain 'B' and resid 981 through 983 No H-bonds generated for 'chain 'B' and resid 981 through 983' Processing helix chain 'B' and resid 997 through 1002 removed outlier: 3.575A pdb=" N GLY B1001 " --> pdb=" O LEU B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1018 Processing helix chain 'C' and resid 15 through 44 removed outlier: 3.835A pdb=" N PHE C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER C 23 " --> pdb=" O PHE C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 93 Processing helix chain 'C' and resid 96 through 122 Processing helix chain 'C' and resid 136 through 160 Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 169 through 188 Proline residue: C 180 - end of helix removed outlier: 3.664A pdb=" N ILE C 186 " --> pdb=" O SER C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 204 removed outlier: 4.050A pdb=" N PHE C 197 " --> pdb=" O GLY C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 213 Processing helix chain 'C' and resid 218 through 249 Processing helix chain 'C' and resid 250 through 254 Processing helix chain 'C' and resid 262 through 275 Processing helix chain 'C' and resid 286 through 317 removed outlier: 3.682A pdb=" N ILE C 301 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N GLY C 302 " --> pdb=" O MET C 298 " (cutoff:3.500A) Proline residue: C 309 - end of helix Processing helix chain 'C' and resid 341 through 353 removed outlier: 3.656A pdb=" N ASP C 351 " --> pdb=" O ASN C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 383 Processing helix chain 'C' and resid 396 through 403 Processing helix chain 'C' and resid 404 through 408 Processing helix chain 'C' and resid 421 through 440 Processing helix chain 'C' and resid 453 through 460 removed outlier: 4.302A pdb=" N TYR C 457 " --> pdb=" O HIS C 453 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU C 458 " --> pdb=" O ASN C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 475 through 489 removed outlier: 3.516A pdb=" N LEU C 488 " --> pdb=" O ALA C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 500 removed outlier: 3.906A pdb=" N LEU C 499 " --> pdb=" O LEU C 495 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE C 500 " --> pdb=" O MET C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 523 Processing helix chain 'C' and resid 532 through 536 Processing helix chain 'C' and resid 539 through 550 Processing helix chain 'C' and resid 592 through 602 removed outlier: 3.629A pdb=" N VAL C 596 " --> pdb=" O SER C 592 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG C 598 " --> pdb=" O GLU C 594 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALA C 599 " --> pdb=" O GLU C 595 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE C 600 " --> pdb=" O VAL C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 607 removed outlier: 3.614A pdb=" N CYS C 606 " --> pdb=" O CYS C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 616 removed outlier: 3.894A pdb=" N ILE C 616 " --> pdb=" O VAL C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 725 Processing helix chain 'C' and resid 728 through 735 Processing helix chain 'C' and resid 756 through 761 Processing helix chain 'C' and resid 762 through 765 removed outlier: 4.068A pdb=" N ALA C 765 " --> pdb=" O PRO C 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 762 through 765' Processing helix chain 'C' and resid 769 through 773 Processing helix chain 'C' and resid 781 through 793 removed outlier: 3.579A pdb=" N ARG C 787 " --> pdb=" O ASP C 783 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS C 790 " --> pdb=" O HIS C 786 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N THR C 791 " --> pdb=" O ARG C 787 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU C 792 " --> pdb=" O GLU C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 814 removed outlier: 3.535A pdb=" N LEU C 811 " --> pdb=" O ASN C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 819 removed outlier: 3.622A pdb=" N CYS C 819 " --> pdb=" O ILE C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 839 through 851 Processing helix chain 'C' and resid 882 through 886 Processing helix chain 'C' and resid 894 through 901 Processing helix chain 'C' and resid 912 through 915 Processing helix chain 'C' and resid 916 through 921 Processing helix chain 'C' and resid 928 through 931 Processing helix chain 'C' and resid 932 through 940 Processing helix chain 'C' and resid 940 through 952 removed outlier: 3.620A pdb=" N LEU C 944 " --> pdb=" O ASN C 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 965 Processing helix chain 'C' and resid 975 through 980 Processing helix chain 'C' and resid 981 through 983 No H-bonds generated for 'chain 'C' and resid 981 through 983' Processing helix chain 'C' and resid 997 through 1002 removed outlier: 3.575A pdb=" N GLY C1001 " --> pdb=" O LEU C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1018 Processing helix chain 'D' and resid 15 through 44 removed outlier: 3.834A pdb=" N PHE D 19 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER D 23 " --> pdb=" O PHE D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 93 Processing helix chain 'D' and resid 96 through 122 Processing helix chain 'D' and resid 136 through 160 Processing helix chain 'D' and resid 162 through 167 Processing helix chain 'D' and resid 169 through 188 Proline residue: D 180 - end of helix removed outlier: 3.665A pdb=" N ILE D 186 " --> pdb=" O SER D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 204 removed outlier: 4.049A pdb=" N PHE D 197 " --> pdb=" O GLY D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 213 Processing helix chain 'D' and resid 218 through 249 Processing helix chain 'D' and resid 250 through 254 Processing helix chain 'D' and resid 262 through 275 Processing helix chain 'D' and resid 286 through 317 removed outlier: 3.682A pdb=" N ILE D 301 " --> pdb=" O ILE D 297 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N GLY D 302 " --> pdb=" O MET D 298 " (cutoff:3.500A) Proline residue: D 309 - end of helix Processing helix chain 'D' and resid 341 through 353 removed outlier: 3.657A pdb=" N ASP D 351 " --> pdb=" O ASN D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 383 Processing helix chain 'D' and resid 396 through 403 Processing helix chain 'D' and resid 404 through 408 Processing helix chain 'D' and resid 421 through 440 Processing helix chain 'D' and resid 453 through 460 removed outlier: 4.301A pdb=" N TYR D 457 " --> pdb=" O HIS D 453 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU D 458 " --> pdb=" O ASN D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 475 through 489 removed outlier: 3.516A pdb=" N LEU D 488 " --> pdb=" O ALA D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 500 removed outlier: 3.905A pdb=" N LEU D 499 " --> pdb=" O LEU D 495 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE D 500 " --> pdb=" O MET D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 523 Processing helix chain 'D' and resid 532 through 536 Processing helix chain 'D' and resid 539 through 550 Processing helix chain 'D' and resid 592 through 602 removed outlier: 3.629A pdb=" N VAL D 596 " --> pdb=" O SER D 592 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG D 598 " --> pdb=" O GLU D 594 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ALA D 599 " --> pdb=" O GLU D 595 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE D 600 " --> pdb=" O VAL D 596 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 607 removed outlier: 3.614A pdb=" N CYS D 606 " --> pdb=" O CYS D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 616 removed outlier: 3.893A pdb=" N ILE D 616 " --> pdb=" O VAL D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 725 Processing helix chain 'D' and resid 728 through 735 Processing helix chain 'D' and resid 756 through 761 Processing helix chain 'D' and resid 762 through 765 removed outlier: 4.068A pdb=" N ALA D 765 " --> pdb=" O PRO D 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 762 through 765' Processing helix chain 'D' and resid 769 through 773 Processing helix chain 'D' and resid 781 through 793 removed outlier: 3.579A pdb=" N ARG D 787 " --> pdb=" O ASP D 783 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS D 790 " --> pdb=" O HIS D 786 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N THR D 791 " --> pdb=" O ARG D 787 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU D 792 " --> pdb=" O GLU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 807 through 814 removed outlier: 3.535A pdb=" N LEU D 811 " --> pdb=" O ASN D 807 " (cutoff:3.500A) Processing helix chain 'D' and resid 815 through 819 removed outlier: 3.622A pdb=" N CYS D 819 " --> pdb=" O ILE D 816 " (cutoff:3.500A) Processing helix chain 'D' and resid 839 through 851 Processing helix chain 'D' and resid 882 through 886 Processing helix chain 'D' and resid 894 through 901 Processing helix chain 'D' and resid 912 through 915 Processing helix chain 'D' and resid 916 through 921 Processing helix chain 'D' and resid 928 through 931 Processing helix chain 'D' and resid 932 through 940 Processing helix chain 'D' and resid 940 through 952 removed outlier: 3.621A pdb=" N LEU D 944 " --> pdb=" O ASN D 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 965 Processing helix chain 'D' and resid 975 through 980 Processing helix chain 'D' and resid 981 through 983 No H-bonds generated for 'chain 'D' and resid 981 through 983' Processing helix chain 'D' and resid 997 through 1002 removed outlier: 3.574A pdb=" N GLY D1001 " --> pdb=" O LEU D 997 " (cutoff:3.500A) Processing helix chain 'D' and resid 1005 through 1018 Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 130 Processing sheet with id=AA2, first strand: chain 'A' and resid 387 through 391 removed outlier: 6.410A pdb=" N VAL A 334 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU A 367 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL A 336 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N HIS A 333 " --> pdb=" O ALA A 410 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N LEU A 412 " --> pdb=" O HIS A 333 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL A 335 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU A 414 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N CYS A 337 " --> pdb=" O LEU A 414 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 525 through 530 removed outlier: 4.493A pdb=" N GLN A 585 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A 557 " --> pdb=" O PHE A 587 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE A 589 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU A 555 " --> pdb=" O ILE A 589 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 708 through 709 Processing sheet with id=AA5, first strand: chain 'A' and resid 798 through 802 removed outlier: 6.483A pdb=" N THR A 776 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LEU A 801 " --> pdb=" O THR A 776 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE A 778 " --> pdb=" O LEU A 801 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N SER A 826 " --> pdb=" O GLU A 891 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 986 through 991 removed outlier: 6.691A pdb=" N GLN A1058 " --> pdb=" O LEU A1024 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU A1024 " --> pdb=" O GLN A1058 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TYR A1060 " --> pdb=" O ILE A1022 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AA8, first strand: chain 'B' and resid 387 through 391 removed outlier: 6.411A pdb=" N VAL B 334 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU B 367 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL B 336 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N HIS B 333 " --> pdb=" O ALA B 410 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N LEU B 412 " --> pdb=" O HIS B 333 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL B 335 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU B 414 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N CYS B 337 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 525 through 530 removed outlier: 4.493A pdb=" N GLN B 585 " --> pdb=" O GLU B 559 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 557 " --> pdb=" O PHE B 587 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE B 589 " --> pdb=" O LEU B 555 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU B 555 " --> pdb=" O ILE B 589 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 708 through 709 Processing sheet with id=AB2, first strand: chain 'B' and resid 798 through 802 removed outlier: 6.483A pdb=" N THR B 776 " --> pdb=" O SER B 799 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LEU B 801 " --> pdb=" O THR B 776 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE B 778 " --> pdb=" O LEU B 801 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N SER B 826 " --> pdb=" O GLU B 891 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 986 through 991 removed outlier: 6.691A pdb=" N GLN B1058 " --> pdb=" O LEU B1024 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU B1024 " --> pdb=" O GLN B1058 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TYR B1060 " --> pdb=" O ILE B1022 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 128 through 130 Processing sheet with id=AB5, first strand: chain 'C' and resid 387 through 391 removed outlier: 6.410A pdb=" N VAL C 334 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU C 367 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL C 336 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N HIS C 333 " --> pdb=" O ALA C 410 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N LEU C 412 " --> pdb=" O HIS C 333 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL C 335 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU C 414 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N CYS C 337 " --> pdb=" O LEU C 414 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 525 through 530 removed outlier: 4.494A pdb=" N GLN C 585 " --> pdb=" O GLU C 559 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA C 557 " --> pdb=" O PHE C 587 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE C 589 " --> pdb=" O LEU C 555 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LEU C 555 " --> pdb=" O ILE C 589 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AB8, first strand: chain 'C' and resid 798 through 802 removed outlier: 6.484A pdb=" N THR C 776 " --> pdb=" O SER C 799 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LEU C 801 " --> pdb=" O THR C 776 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE C 778 " --> pdb=" O LEU C 801 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N SER C 826 " --> pdb=" O GLU C 891 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 986 through 991 removed outlier: 6.691A pdb=" N GLN C1058 " --> pdb=" O LEU C1024 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU C1024 " --> pdb=" O GLN C1058 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TYR C1060 " --> pdb=" O ILE C1022 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 128 through 130 Processing sheet with id=AC2, first strand: chain 'D' and resid 387 through 391 removed outlier: 6.410A pdb=" N VAL D 334 " --> pdb=" O VAL D 365 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU D 367 " --> pdb=" O VAL D 334 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL D 336 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N HIS D 333 " --> pdb=" O ALA D 410 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N LEU D 412 " --> pdb=" O HIS D 333 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL D 335 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU D 414 " --> pdb=" O VAL D 335 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N CYS D 337 " --> pdb=" O LEU D 414 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 525 through 530 removed outlier: 4.494A pdb=" N GLN D 585 " --> pdb=" O GLU D 559 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA D 557 " --> pdb=" O PHE D 587 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE D 589 " --> pdb=" O LEU D 555 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU D 555 " --> pdb=" O ILE D 589 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 708 through 709 Processing sheet with id=AC5, first strand: chain 'D' and resid 798 through 802 removed outlier: 6.483A pdb=" N THR D 776 " --> pdb=" O SER D 799 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LEU D 801 " --> pdb=" O THR D 776 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE D 778 " --> pdb=" O LEU D 801 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N SER D 826 " --> pdb=" O GLU D 891 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 986 through 991 removed outlier: 6.691A pdb=" N GLN D1058 " --> pdb=" O LEU D1024 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU D1024 " --> pdb=" O GLN D1058 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TYR D1060 " --> pdb=" O ILE D1022 " (cutoff:3.500A) 1480 hydrogen bonds defined for protein. 3996 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: 6.21 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5161 1.32 - 1.44: 7660 1.44 - 1.57: 16027 1.57 - 1.70: 0 1.70 - 1.83: 268 Bond restraints: 29116 Sorted by residual: bond pdb=" CA ASP A 189 " pdb=" CB ASP A 189 " ideal model delta sigma weight residual 1.523 1.454 0.070 1.21e-02 6.83e+03 3.30e+01 bond pdb=" CA ASP D 189 " pdb=" CB ASP D 189 " ideal model delta sigma weight residual 1.523 1.454 0.069 1.21e-02 6.83e+03 3.28e+01 bond pdb=" CA ASP C 189 " pdb=" CB ASP C 189 " ideal model delta sigma weight residual 1.523 1.454 0.069 1.21e-02 6.83e+03 3.28e+01 bond pdb=" CA ASP B 189 " pdb=" CB ASP B 189 " ideal model delta sigma weight residual 1.523 1.454 0.069 1.21e-02 6.83e+03 3.28e+01 bond pdb=" CA LEU A1014 " pdb=" C LEU A1014 " ideal model delta sigma weight residual 1.523 1.459 0.064 1.30e-02 5.92e+03 2.43e+01 ... (remaining 29111 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 27341 1.64 - 3.27: 9949 3.27 - 4.91: 1987 4.91 - 6.54: 280 6.54 - 8.18: 43 Bond angle restraints: 39600 Sorted by residual: angle pdb=" OE1 GLN B 917 " pdb=" CD GLN B 917 " pdb=" NE2 GLN B 917 " ideal model delta sigma weight residual 122.60 115.83 6.77 1.00e+00 1.00e+00 4.59e+01 angle pdb=" OE1 GLN C 917 " pdb=" CD GLN C 917 " pdb=" NE2 GLN C 917 " ideal model delta sigma weight residual 122.60 115.83 6.77 1.00e+00 1.00e+00 4.58e+01 angle pdb=" OE1 GLN D 917 " pdb=" CD GLN D 917 " pdb=" NE2 GLN D 917 " ideal model delta sigma weight residual 122.60 115.83 6.77 1.00e+00 1.00e+00 4.58e+01 angle pdb=" OE1 GLN A 917 " pdb=" CD GLN A 917 " pdb=" NE2 GLN A 917 " ideal model delta sigma weight residual 122.60 115.84 6.76 1.00e+00 1.00e+00 4.56e+01 angle pdb=" CA ASP C 189 " pdb=" CB ASP C 189 " pdb=" CG ASP C 189 " ideal model delta sigma weight residual 112.60 118.80 -6.20 1.00e+00 1.00e+00 3.84e+01 ... (remaining 39595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 15917 17.99 - 35.98: 958 35.98 - 53.97: 129 53.97 - 71.96: 52 71.96 - 89.95: 24 Dihedral angle restraints: 17080 sinusoidal: 6524 harmonic: 10556 Sorted by residual: dihedral pdb=" CA GLY B 370 " pdb=" C GLY B 370 " pdb=" N LEU B 371 " pdb=" CA LEU B 371 " ideal model delta harmonic sigma weight residual 180.00 153.20 26.80 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA GLY C 370 " pdb=" C GLY C 370 " pdb=" N LEU C 371 " pdb=" CA LEU C 371 " ideal model delta harmonic sigma weight residual 180.00 153.20 26.80 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA GLY D 370 " pdb=" C GLY D 370 " pdb=" N LEU D 371 " pdb=" CA LEU D 371 " ideal model delta harmonic sigma weight residual 180.00 153.21 26.79 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 17077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 3917 0.133 - 0.267: 547 0.267 - 0.400: 28 0.400 - 0.533: 16 0.533 - 0.667: 8 Chirality restraints: 4516 Sorted by residual: chirality pdb=" CG LEU C1014 " pdb=" CB LEU C1014 " pdb=" CD1 LEU C1014 " pdb=" CD2 LEU C1014 " both_signs ideal model delta sigma weight residual False -2.59 -1.92 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CG LEU D1014 " pdb=" CB LEU D1014 " pdb=" CD1 LEU D1014 " pdb=" CD2 LEU D1014 " both_signs ideal model delta sigma weight residual False -2.59 -1.92 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CG LEU B1014 " pdb=" CB LEU B1014 " pdb=" CD1 LEU B1014 " pdb=" CD2 LEU B1014 " both_signs ideal model delta sigma weight residual False -2.59 -1.92 -0.66 2.00e-01 2.50e+01 1.10e+01 ... (remaining 4513 not shown) Planarity restraints: 5016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 167 " -0.116 2.00e-02 2.50e+03 5.72e-02 8.19e+01 pdb=" CG TRP B 167 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP B 167 " 0.057 2.00e-02 2.50e+03 pdb=" CD2 TRP B 167 " 0.026 2.00e-02 2.50e+03 pdb=" NE1 TRP B 167 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TRP B 167 " -0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP B 167 " 0.075 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 167 " -0.064 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 167 " 0.035 2.00e-02 2.50e+03 pdb=" CH2 TRP B 167 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 167 " 0.116 2.00e-02 2.50e+03 5.72e-02 8.19e+01 pdb=" CG TRP D 167 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP D 167 " -0.056 2.00e-02 2.50e+03 pdb=" CD2 TRP D 167 " -0.027 2.00e-02 2.50e+03 pdb=" NE1 TRP D 167 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TRP D 167 " 0.015 2.00e-02 2.50e+03 pdb=" CE3 TRP D 167 " -0.076 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 167 " 0.064 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 167 " -0.034 2.00e-02 2.50e+03 pdb=" CH2 TRP D 167 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 167 " -0.115 2.00e-02 2.50e+03 5.72e-02 8.18e+01 pdb=" CG TRP A 167 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP A 167 " 0.056 2.00e-02 2.50e+03 pdb=" CD2 TRP A 167 " 0.026 2.00e-02 2.50e+03 pdb=" NE1 TRP A 167 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TRP A 167 " -0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP A 167 " 0.076 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 167 " -0.064 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 167 " 0.034 2.00e-02 2.50e+03 pdb=" CH2 TRP A 167 " -0.053 2.00e-02 2.50e+03 ... (remaining 5013 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.85: 8619 2.85 - 3.42: 32742 3.42 - 3.99: 55041 3.99 - 4.57: 76366 4.57 - 5.14: 113086 Nonbonded interactions: 285854 Sorted by model distance: nonbonded pdb=" CG2 THR C 273 " pdb=" CZ PHE D 279 " model vdw 2.277 3.760 nonbonded pdb=" CG2 THR A 273 " pdb=" CZ PHE B 279 " model vdw 2.287 3.760 nonbonded pdb=" CG2 THR B 273 " pdb=" CZ PHE C 279 " model vdw 2.300 3.760 nonbonded pdb=" CZ PHE A 279 " pdb=" CG2 THR D 273 " model vdw 2.325 3.760 nonbonded pdb=" O GLY B 12 " pdb=" C ASP B 13 " model vdw 2.345 3.270 ... (remaining 285849 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' selection = (chain 'B' and resid 8 through 1065) selection = (chain 'C' and resid 8 through 1065) 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 26.220 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 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 : 0.013 0.117 29116 Z= 0.784 Angle : 1.691 8.175 39600 Z= 1.141 Chirality : 0.097 0.667 4516 Planarity : 0.012 0.059 5016 Dihedral : 12.910 89.946 10256 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.56 % Favored : 96.42 % Rotamer: Outliers : 0.75 % Allowed : 4.26 % Favored : 94.99 % Cbeta Deviations : 0.59 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.13), residues: 3572 helix: -1.20 (0.11), residues: 1828 sheet: 0.03 (0.25), residues: 408 loop : 0.02 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1028 TYR 0.113 0.017 TYR C 938 PHE 0.083 0.012 PHE C 500 TRP 0.116 0.019 TRP D 167 HIS 0.011 0.003 HIS C 607 Details of bonding type rmsd/Z covalent geometry : bond 0.01266 / 0.78 (29116) covalent geometry : angle 1.69119 / 1.14 (39600) hydrogen bonds : bond 0.16354 / 10.70 ( 1480) hydrogen bonds : angle 7.31408 / 5.32 ( 3996) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 1.143 Fit side-chains REVERT: A 713 MET cc_start: 0.9101 (mmt) cc_final: 0.8802 (mmt) REVERT: A 852 MET cc_start: 0.9056 (mtp) cc_final: 0.8839 (mtm) REVERT: B 713 MET cc_start: 0.9063 (mmt) cc_final: 0.8843 (mmt) outliers start: 23 outliers final: 4 residues processed: 161 average time/residue: 0.8535 time to fit residues: 156.8275 Evaluate side-chains 101 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain D residue 287 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 6.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN A 831 ASN A 885 ASN B 347 ASN B 831 ASN B 885 ASN C 347 ASN C 416 ASN C 831 ASN C 885 ASN D 347 ASN D 831 ASN D 885 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.065925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.047979 restraints weight = 80254.150| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 3.08 r_work: 0.2592 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29116 Z= 0.191 Angle : 0.590 7.091 39600 Z= 0.310 Chirality : 0.044 0.186 4516 Planarity : 0.004 0.033 5016 Dihedral : 5.050 33.738 3884 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.08 % Allowed : 7.70 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.14), residues: 3572 helix: 0.53 (0.12), residues: 1804 sheet: 0.12 (0.24), residues: 464 loop : 0.78 (0.19), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 808 TYR 0.017 0.001 TYR D 505 PHE 0.018 0.001 PHE B 107 TRP 0.017 0.002 TRP C 514 HIS 0.008 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (29116) covalent geometry : angle 0.58991 / 0.31 (39600) hydrogen bonds : bond 0.05033 / 3.23 ( 1480) hydrogen bonds : angle 4.80583 / 3.49 ( 3996) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 1.004 Fit side-chains REVERT: A 313 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8490 (tt0) REVERT: A 488 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9171 (mt) REVERT: A 713 MET cc_start: 0.9203 (mmt) cc_final: 0.8969 (mmt) REVERT: B 313 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8466 (tt0) REVERT: B 488 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9151 (mt) REVERT: B 713 MET cc_start: 0.9188 (mmt) cc_final: 0.8985 (mmt) REVERT: C 313 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8506 (tt0) REVERT: C 488 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9154 (mt) REVERT: C 502 MET cc_start: 0.9085 (mmm) cc_final: 0.8879 (mmm) REVERT: D 313 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8479 (tt0) REVERT: D 488 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9135 (mt) outliers start: 33 outliers final: 4 residues processed: 130 average time/residue: 0.7502 time to fit residues: 113.3275 Evaluate side-chains 107 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 488 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 298 optimal weight: 0.4980 chunk 308 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 335 optimal weight: 7.9990 chunk 255 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 345 optimal weight: 0.0870 chunk 312 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 301 optimal weight: 7.9990 chunk 113 optimal weight: 0.9980 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 ASN ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 836 ASN B 897 ASN ** C 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 897 ASN ** D 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 897 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.067042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.049345 restraints weight = 80703.330| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 3.09 r_work: 0.2634 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 29116 Z= 0.107 Angle : 0.501 6.759 39600 Z= 0.259 Chirality : 0.040 0.149 4516 Planarity : 0.003 0.034 5016 Dihedral : 4.420 29.247 3884 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.21 % Allowed : 7.86 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.15), residues: 3572 helix: 0.96 (0.13), residues: 1832 sheet: 0.19 (0.24), residues: 464 loop : 0.89 (0.19), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 706 TYR 0.011 0.001 TYR D 505 PHE 0.012 0.001 PHE D 500 TRP 0.015 0.001 TRP B 514 HIS 0.005 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (29116) covalent geometry : angle 0.50137 / 0.26 (39600) hydrogen bonds : bond 0.04049 / 2.60 ( 1480) hydrogen bonds : angle 4.32352 / 3.12 ( 3996) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 1.107 Fit side-chains REVERT: B 488 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.9016 (mt) REVERT: B 733 SER cc_start: 0.9406 (OUTLIER) cc_final: 0.8957 (p) REVERT: D 733 SER cc_start: 0.9409 (OUTLIER) cc_final: 0.8960 (p) outliers start: 37 outliers final: 14 residues processed: 120 average time/residue: 0.6946 time to fit residues: 97.6907 Evaluate side-chains 109 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 1043 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 1043 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 814 VAL Chi-restraints excluded: chain D residue 947 ILE Chi-restraints excluded: chain D residue 1043 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 147 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 346 optimal weight: 8.9990 chunk 159 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 280 optimal weight: 2.9990 chunk 352 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 290 optimal weight: 8.9990 chunk 214 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 ASN ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 836 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.065723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.047524 restraints weight = 80698.020| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 3.11 r_work: 0.2580 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 29116 Z= 0.167 Angle : 0.517 7.904 39600 Z= 0.267 Chirality : 0.041 0.184 4516 Planarity : 0.003 0.033 5016 Dihedral : 4.302 33.080 3884 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.47 % Allowed : 8.36 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.15), residues: 3572 helix: 1.06 (0.13), residues: 1828 sheet: 0.18 (0.24), residues: 460 loop : 0.85 (0.19), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 706 TYR 0.012 0.001 TYR A 938 PHE 0.015 0.001 PHE B 107 TRP 0.011 0.001 TRP C 514 HIS 0.005 0.001 HIS C 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (29116) covalent geometry : angle 0.51726 / 0.27 (39600) hydrogen bonds : bond 0.04243 / 2.73 ( 1480) hydrogen bonds : angle 4.26299 / 3.07 ( 3996) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 93 time to evaluate : 1.202 Fit side-chains REVERT: A 733 SER cc_start: 0.9395 (OUTLIER) cc_final: 0.8940 (p) REVERT: B 488 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9084 (mt) REVERT: C 496 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8946 (tpp) REVERT: C 502 MET cc_start: 0.9118 (mmm) cc_final: 0.8910 (mmm) REVERT: C 733 SER cc_start: 0.9414 (OUTLIER) cc_final: 0.8975 (p) outliers start: 45 outliers final: 21 residues processed: 121 average time/residue: 0.6156 time to fit residues: 89.1655 Evaluate side-chains 117 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 1043 VAL Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 947 ILE Chi-restraints excluded: chain C residue 1043 VAL Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 814 VAL Chi-restraints excluded: chain D residue 947 ILE Chi-restraints excluded: chain D residue 1043 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 39 optimal weight: 3.9990 chunk 257 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 251 optimal weight: 2.9990 chunk 317 optimal weight: 2.9990 chunk 249 optimal weight: 6.9990 chunk 280 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 225 optimal weight: 0.7980 chunk 145 optimal weight: 0.0770 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 836 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.066866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.048991 restraints weight = 79933.676| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 3.07 r_work: 0.2620 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 29116 Z= 0.115 Angle : 0.475 6.972 39600 Z= 0.244 Chirality : 0.040 0.156 4516 Planarity : 0.003 0.035 5016 Dihedral : 4.121 35.397 3884 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.54 % Allowed : 9.40 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.15), residues: 3572 helix: 1.18 (0.13), residues: 1828 sheet: 0.20 (0.24), residues: 460 loop : 0.90 (0.19), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 706 TYR 0.010 0.001 TYR A 938 PHE 0.013 0.001 PHE B 107 TRP 0.010 0.001 TRP B 514 HIS 0.003 0.001 HIS D 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (29116) covalent geometry : angle 0.47535 / 0.24 (39600) hydrogen bonds : bond 0.03812 / 2.45 ( 1480) hydrogen bonds : angle 4.11432 / 2.96 ( 3996) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 95 time to evaluate : 1.082 Fit side-chains REVERT: A 733 SER cc_start: 0.9383 (OUTLIER) cc_final: 0.8926 (p) REVERT: B 508 THR cc_start: 0.8468 (OUTLIER) cc_final: 0.8070 (p) REVERT: B 511 MET cc_start: 0.8030 (mtm) cc_final: 0.7751 (mtm) REVERT: C 502 MET cc_start: 0.9106 (mmm) cc_final: 0.8869 (mmm) REVERT: C 508 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.8169 (p) REVERT: C 733 SER cc_start: 0.9400 (OUTLIER) cc_final: 0.8945 (p) REVERT: D 508 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8223 (p) outliers start: 47 outliers final: 25 residues processed: 125 average time/residue: 0.6119 time to fit residues: 91.7919 Evaluate side-chains 123 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain B residue 1043 VAL Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 947 ILE Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 519 MET Chi-restraints excluded: chain D residue 814 VAL Chi-restraints excluded: chain D residue 947 ILE Chi-restraints excluded: chain D residue 1043 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 104 optimal weight: 4.9990 chunk 250 optimal weight: 20.0000 chunk 34 optimal weight: 0.9990 chunk 157 optimal weight: 0.3980 chunk 247 optimal weight: 0.9990 chunk 222 optimal weight: 0.0670 chunk 312 optimal weight: 0.0970 chunk 111 optimal weight: 7.9990 chunk 163 optimal weight: 2.9990 chunk 350 optimal weight: 5.9990 chunk 342 optimal weight: 1.9990 overall best weight: 0.5120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 HIS B 243 HIS C 243 HIS D 243 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.069364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.051292 restraints weight = 78953.266| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 3.09 r_work: 0.2679 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 29116 Z= 0.086 Angle : 0.454 8.594 39600 Z= 0.232 Chirality : 0.038 0.135 4516 Planarity : 0.003 0.037 5016 Dihedral : 3.853 30.781 3884 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.95 % Allowed : 9.93 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.15), residues: 3572 helix: 1.34 (0.13), residues: 1824 sheet: -0.15 (0.23), residues: 508 loop : 1.18 (0.19), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 706 TYR 0.009 0.001 TYR B 938 PHE 0.012 0.001 PHE A 304 TRP 0.010 0.001 TRP C 514 HIS 0.002 0.000 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00171 / 0.09 (29116) covalent geometry : angle 0.45382 / 0.23 (39600) hydrogen bonds : bond 0.03345 / 2.15 ( 1480) hydrogen bonds : angle 3.94209 / 2.83 ( 3996) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 1.220 Fit side-chains REVERT: A 733 SER cc_start: 0.9362 (OUTLIER) cc_final: 0.8920 (p) REVERT: B 508 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.7959 (p) REVERT: B 511 MET cc_start: 0.8084 (mtm) cc_final: 0.7716 (mtm) REVERT: B 713 MET cc_start: 0.9195 (mmt) cc_final: 0.8964 (mmt) REVERT: C 502 MET cc_start: 0.9015 (mmm) cc_final: 0.8757 (mmm) REVERT: C 733 SER cc_start: 0.9375 (OUTLIER) cc_final: 0.8920 (p) REVERT: D 274 MET cc_start: 0.9240 (OUTLIER) cc_final: 0.9039 (ptp) REVERT: D 502 MET cc_start: 0.8819 (mmp) cc_final: 0.8369 (mmm) outliers start: 29 outliers final: 10 residues processed: 122 average time/residue: 0.6698 time to fit residues: 96.8453 Evaluate side-chains 110 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 519 MET Chi-restraints excluded: chain D residue 814 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 290 optimal weight: 1.9990 chunk 203 optimal weight: 0.7980 chunk 84 optimal weight: 9.9990 chunk 202 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 327 optimal weight: 20.0000 chunk 311 optimal weight: 0.2980 chunk 268 optimal weight: 2.9990 chunk 300 optimal weight: 5.9990 chunk 342 optimal weight: 0.6980 chunk 276 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.068972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.050862 restraints weight = 79164.477| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 3.10 r_work: 0.2667 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29116 Z= 0.093 Angle : 0.462 9.504 39600 Z= 0.234 Chirality : 0.039 0.142 4516 Planarity : 0.003 0.037 5016 Dihedral : 3.729 27.373 3884 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.05 % Allowed : 10.22 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.15), residues: 3572 helix: 1.39 (0.13), residues: 1828 sheet: -0.14 (0.24), residues: 508 loop : 1.17 (0.19), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 706 TYR 0.010 0.001 TYR A 938 PHE 0.012 0.001 PHE D 304 TRP 0.010 0.001 TRP A 80 HIS 0.002 0.000 HIS B 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 (29116) covalent geometry : angle 0.46187 / 0.23 (39600) hydrogen bonds : bond 0.03383 / 2.17 ( 1480) hydrogen bonds : angle 3.89496 / 2.79 ( 3996) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 1.151 Fit side-chains REVERT: A 252 PHE cc_start: 0.9352 (OUTLIER) cc_final: 0.9121 (p90) REVERT: A 496 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8922 (tpp) REVERT: A 733 SER cc_start: 0.9376 (OUTLIER) cc_final: 0.8933 (p) REVERT: B 252 PHE cc_start: 0.9363 (OUTLIER) cc_final: 0.9117 (p90) REVERT: B 508 THR cc_start: 0.8465 (OUTLIER) cc_final: 0.7931 (p) REVERT: B 511 MET cc_start: 0.8205 (mtm) cc_final: 0.7863 (mtm) REVERT: B 733 SER cc_start: 0.9373 (OUTLIER) cc_final: 0.8935 (p) REVERT: C 252 PHE cc_start: 0.9361 (OUTLIER) cc_final: 0.9112 (p90) REVERT: C 496 MET cc_start: 0.9262 (mtp) cc_final: 0.9022 (mmm) REVERT: C 502 MET cc_start: 0.9049 (mmm) cc_final: 0.8704 (mmm) REVERT: C 733 SER cc_start: 0.9375 (OUTLIER) cc_final: 0.8935 (p) REVERT: D 252 PHE cc_start: 0.9370 (OUTLIER) cc_final: 0.9115 (p90) REVERT: D 496 MET cc_start: 0.9157 (ttm) cc_final: 0.8948 (tpp) REVERT: D 502 MET cc_start: 0.8847 (mmp) cc_final: 0.8378 (mmm) REVERT: D 733 SER cc_start: 0.9375 (OUTLIER) cc_final: 0.8934 (p) outliers start: 32 outliers final: 15 residues processed: 126 average time/residue: 0.6485 time to fit residues: 97.5577 Evaluate side-chains 122 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 519 MET Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 814 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 31 optimal weight: 0.0070 chunk 157 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 190 optimal weight: 6.9990 chunk 355 optimal weight: 10.0000 chunk 254 optimal weight: 0.7980 chunk 332 optimal weight: 0.1980 chunk 46 optimal weight: 10.0000 chunk 347 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.069927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.051970 restraints weight = 79265.166| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 3.10 r_work: 0.2698 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 29116 Z= 0.084 Angle : 0.449 8.583 39600 Z= 0.226 Chirality : 0.038 0.132 4516 Planarity : 0.003 0.037 5016 Dihedral : 3.571 19.303 3884 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.98 % Allowed : 10.52 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.15), residues: 3572 helix: 1.39 (0.13), residues: 1848 sheet: -0.11 (0.24), residues: 508 loop : 1.15 (0.19), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 357 TYR 0.009 0.001 TYR D 938 PHE 0.011 0.001 PHE D 304 TRP 0.013 0.001 TRP A 80 HIS 0.002 0.000 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00172 / 0.08 (29116) covalent geometry : angle 0.44870 / 0.23 (39600) hydrogen bonds : bond 0.03182 / 2.04 ( 1480) hydrogen bonds : angle 3.80771 / 2.73 ( 3996) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.949 Fit side-chains REVERT: A 511 MET cc_start: 0.7905 (mtm) cc_final: 0.7671 (ptm) REVERT: A 733 SER cc_start: 0.9324 (OUTLIER) cc_final: 0.8863 (p) REVERT: A 993 PHE cc_start: 0.9120 (t80) cc_final: 0.8851 (t80) REVERT: B 252 PHE cc_start: 0.9341 (OUTLIER) cc_final: 0.9138 (p90) REVERT: B 508 THR cc_start: 0.8530 (OUTLIER) cc_final: 0.7934 (p) REVERT: C 252 PHE cc_start: 0.9344 (OUTLIER) cc_final: 0.9139 (p90) REVERT: C 496 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8973 (mmm) REVERT: C 502 MET cc_start: 0.9025 (mmm) cc_final: 0.8809 (mmm) REVERT: C 508 THR cc_start: 0.8272 (OUTLIER) cc_final: 0.8004 (p) REVERT: D 252 PHE cc_start: 0.9347 (OUTLIER) cc_final: 0.9135 (p90) REVERT: D 274 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.9012 (ptp) REVERT: D 508 THR cc_start: 0.8281 (OUTLIER) cc_final: 0.8000 (p) outliers start: 30 outliers final: 10 residues processed: 131 average time/residue: 0.6074 time to fit residues: 94.5716 Evaluate side-chains 116 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 814 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 101 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 302 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 328 optimal weight: 0.0030 chunk 239 optimal weight: 9.9990 chunk 132 optimal weight: 0.0670 chunk 1 optimal weight: 8.9990 chunk 321 optimal weight: 5.9990 overall best weight: 2.4134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.067515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.049169 restraints weight = 79925.369| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 3.11 r_work: 0.2619 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29116 Z= 0.142 Angle : 0.494 10.057 39600 Z= 0.250 Chirality : 0.040 0.172 4516 Planarity : 0.003 0.036 5016 Dihedral : 3.690 18.538 3882 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.82 % Allowed : 10.85 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.15), residues: 3572 helix: 1.37 (0.13), residues: 1836 sheet: -0.10 (0.24), residues: 504 loop : 1.04 (0.19), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 706 TYR 0.010 0.001 TYR A 938 PHE 0.017 0.001 PHE C 500 TRP 0.009 0.001 TRP C 80 HIS 0.002 0.001 HIS C 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (29116) covalent geometry : angle 0.49425 / 0.25 (39600) hydrogen bonds : bond 0.03732 / 2.40 ( 1480) hydrogen bonds : angle 3.93115 / 2.82 ( 3996) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 1.163 Fit side-chains REVERT: A 511 MET cc_start: 0.8020 (mtm) cc_final: 0.7802 (ptp) REVERT: A 733 SER cc_start: 0.9363 (OUTLIER) cc_final: 0.8923 (p) REVERT: A 993 PHE cc_start: 0.9140 (t80) cc_final: 0.8845 (t80) REVERT: B 502 MET cc_start: 0.9158 (mmm) cc_final: 0.8430 (mmm) REVERT: B 733 SER cc_start: 0.9384 (OUTLIER) cc_final: 0.8946 (p) REVERT: B 993 PHE cc_start: 0.9155 (t80) cc_final: 0.8854 (t80) REVERT: C 496 MET cc_start: 0.9277 (OUTLIER) cc_final: 0.9020 (mmm) REVERT: C 502 MET cc_start: 0.9046 (mmm) cc_final: 0.8819 (mmm) REVERT: C 508 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8156 (p) REVERT: C 524 MET cc_start: 0.8846 (mmt) cc_final: 0.8401 (mmt) REVERT: C 733 SER cc_start: 0.9383 (OUTLIER) cc_final: 0.8944 (p) REVERT: C 993 PHE cc_start: 0.9151 (t80) cc_final: 0.8849 (t80) REVERT: D 508 THR cc_start: 0.8360 (OUTLIER) cc_final: 0.8128 (p) REVERT: D 733 SER cc_start: 0.9385 (OUTLIER) cc_final: 0.8944 (p) REVERT: D 993 PHE cc_start: 0.9148 (t80) cc_final: 0.8847 (t80) outliers start: 25 outliers final: 8 residues processed: 118 average time/residue: 0.6704 time to fit residues: 93.7497 Evaluate side-chains 115 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 814 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 73 optimal weight: 2.9990 chunk 247 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 199 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 226 optimal weight: 0.8980 chunk 202 optimal weight: 1.9990 chunk 188 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 249 optimal weight: 5.9990 chunk 252 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.069069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.050870 restraints weight = 79537.515| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 3.12 r_work: 0.2667 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 29116 Z= 0.090 Angle : 0.475 10.405 39600 Z= 0.237 Chirality : 0.038 0.137 4516 Planarity : 0.003 0.037 5016 Dihedral : 3.600 20.049 3880 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.52 % Allowed : 11.30 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.15), residues: 3572 helix: 1.45 (0.13), residues: 1828 sheet: -0.13 (0.24), residues: 504 loop : 1.10 (0.19), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 706 TYR 0.009 0.001 TYR B 938 PHE 0.011 0.001 PHE D 304 TRP 0.016 0.001 TRP D 80 HIS 0.002 0.000 HIS C 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.09 (29116) covalent geometry : angle 0.47491 / 0.24 (39600) hydrogen bonds : bond 0.03334 / 2.14 ( 1480) hydrogen bonds : angle 3.85219 / 2.76 ( 3996) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7144 Ramachandran restraints generated. 3572 Oldfield, 0 Emsley, 3572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 1.206 Fit side-chains REVERT: A 511 MET cc_start: 0.8055 (mtm) cc_final: 0.7851 (ptp) REVERT: A 733 SER cc_start: 0.9358 (OUTLIER) cc_final: 0.8915 (p) REVERT: A 993 PHE cc_start: 0.9119 (t80) cc_final: 0.8838 (t80) REVERT: B 502 MET cc_start: 0.9079 (mmm) cc_final: 0.8402 (mmm) REVERT: B 733 SER cc_start: 0.9378 (OUTLIER) cc_final: 0.8938 (p) REVERT: B 993 PHE cc_start: 0.9151 (t80) cc_final: 0.8859 (t80) REVERT: C 496 MET cc_start: 0.9241 (OUTLIER) cc_final: 0.8937 (mmm) REVERT: C 502 MET cc_start: 0.9003 (mmm) cc_final: 0.8681 (mmm) REVERT: C 508 THR cc_start: 0.8343 (OUTLIER) cc_final: 0.8095 (p) REVERT: C 524 MET cc_start: 0.8834 (mmt) cc_final: 0.8406 (mmt) REVERT: C 993 PHE cc_start: 0.9137 (t80) cc_final: 0.8837 (t80) REVERT: D 274 MET cc_start: 0.9214 (OUTLIER) cc_final: 0.8993 (ptp) REVERT: D 508 THR cc_start: 0.8383 (OUTLIER) cc_final: 0.8152 (p) REVERT: D 993 PHE cc_start: 0.9129 (t80) cc_final: 0.8832 (t80) outliers start: 16 outliers final: 7 residues processed: 117 average time/residue: 0.7207 time to fit residues: 99.3309 Evaluate side-chains 113 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 733 SER Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain B residue 733 SER Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain C residue 947 ILE Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 814 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 320 optimal weight: 0.4980 chunk 250 optimal weight: 20.0000 chunk 347 optimal weight: 0.8980 chunk 240 optimal weight: 8.9990 chunk 305 optimal weight: 6.9990 chunk 273 optimal weight: 20.0000 chunk 162 optimal weight: 0.0040 chunk 139 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.067846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.049501 restraints weight = 79978.208| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 3.12 r_work: 0.2630 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29116 Z= 0.120 Angle : 0.491 10.821 39600 Z= 0.245 Chirality : 0.039 0.158 4516 Planarity : 0.003 0.037 5016 Dihedral : 3.632 19.277 3880 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.46 % Allowed : 11.57 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.15), residues: 3572 helix: 1.40 (0.13), residues: 1836 sheet: -0.13 (0.24), residues: 504 loop : 1.00 (0.19), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 706 TYR 0.010 0.001 TYR A 938 PHE 0.012 0.001 PHE B 107 TRP 0.010 0.001 TRP B 80 HIS 0.002 0.001 HIS C 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (29116) covalent geometry : angle 0.49088 / 0.25 (39600) hydrogen bonds : bond 0.03597 / 2.31 ( 1480) hydrogen bonds : angle 3.90399 / 2.79 ( 3996) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5781.39 seconds wall clock time: 100 minutes 11.15 seconds (6011.15 seconds total)