Starting phenix.real_space_refine on Mon Aug 25 13:34:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dic_46903/08_2025/9dic_46903.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dic_46903/08_2025/9dic_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 { model { file = "/net/cci-nas-00/data/ceres_data/9dic_46903/08_2025/9dic_46903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dic_46903/08_2025/9dic_46903.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dic_46903/08_2025/9dic_46903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dic_46903/08_2025/9dic_46903.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.74, per 1000 atoms: 0.20 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: 1.83 Conformation dependent library (CDL) restraints added in 946.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.13 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: 6.05 Time building geometry restraints manager: 2.34 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.330 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 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:7.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 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 aren 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 covalent geometry : bond 0.01266 (29116) covalent geometry : angle 1.69119 (39600) hydrogen bonds : bond 0.16354 ( 1480) hydrogen bonds : angle 7.31408 ( 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 : 0.994 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: 0.7852 time to fit residues: 143.4492 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 : 0.858 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3207 r_free = 0.3207 target = 0.065798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.047822 restraints weight = 80304.196| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 3.08 r_work: 0.2586 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29116 Z= 0.188 Angle : 0.593 7.499 39600 Z= 0.313 Chirality : 0.044 0.185 4516 Planarity : 0.004 0.033 5016 Dihedral : 5.105 34.359 3884 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.02 % Allowed : 7.80 % Favored : 91.19 % 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 aren not related in a simple way. whole: 0.64 (0.14), residues: 3572 helix: 0.52 (0.12), residues: 1796 sheet: 0.11 (0.24), residues: 464 loop : 0.72 (0.19), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 808 TYR 0.017 0.001 TYR D 505 PHE 0.019 0.001 PHE B 107 TRP 0.018 0.002 TRP B 514 HIS 0.007 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00437 (29116) covalent geometry : angle 0.59272 (39600) hydrogen bonds : bond 0.05198 ( 1480) hydrogen bonds : angle 4.86033 ( 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 133 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 1.171 Fit side-chains REVERT: A 313 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8493 (tt0) REVERT: A 488 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9160 (mt) REVERT: A 502 MET cc_start: 0.8841 (mmp) cc_final: 0.8475 (mmm) REVERT: A 713 MET cc_start: 0.9179 (mmt) cc_final: 0.8952 (mmt) REVERT: B 488 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9143 (mt) REVERT: B 713 MET cc_start: 0.9176 (mmt) cc_final: 0.8969 (mmt) REVERT: C 488 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9141 (mt) REVERT: C 502 MET cc_start: 0.9135 (mmm) cc_final: 0.8590 (mmm) REVERT: C 713 MET cc_start: 0.9182 (mmt) cc_final: 0.8929 (mmt) REVERT: D 488 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9126 (mt) REVERT: D 502 MET cc_start: 0.8750 (mmp) cc_final: 0.8490 (mmm) REVERT: D 713 MET cc_start: 0.9196 (mmt) cc_final: 0.8947 (mmt) outliers start: 31 outliers final: 4 residues processed: 130 average time/residue: 0.7063 time to fit residues: 106.6106 Evaluate side-chains 105 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 488 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain D residue 287 VAL 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: 5.9990 chunk 308 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 335 optimal weight: 9.9990 chunk 255 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 345 optimal weight: 7.9990 chunk 312 optimal weight: 4.9990 chunk 212 optimal weight: 10.0000 chunk 301 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 ASN B 416 ASN B 794 ASN ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 836 ASN B 897 ASN C 794 ASN C 831 ASN C 897 ASN D 794 ASN ** D 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 897 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.065339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.046693 restraints weight = 80830.213| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 3.15 r_work: 0.2551 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 29116 Z= 0.236 Angle : 0.575 7.722 39600 Z= 0.299 Chirality : 0.044 0.202 4516 Planarity : 0.004 0.032 5016 Dihedral : 4.732 38.629 3884 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.08 % Allowed : 8.52 % Favored : 90.40 % 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 aren not related in a simple way. whole: 0.87 (0.15), residues: 3572 helix: 0.80 (0.13), residues: 1832 sheet: 0.07 (0.24), residues: 460 loop : 0.75 (0.19), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 706 TYR 0.013 0.001 TYR C 505 PHE 0.015 0.001 PHE A 107 TRP 0.015 0.001 TRP B 514 HIS 0.006 0.001 HIS B 354 Details of bonding type rmsd covalent geometry : bond 0.00555 (29116) covalent geometry : angle 0.57528 (39600) hydrogen bonds : bond 0.04850 ( 1480) hydrogen bonds : angle 4.54564 ( 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 129 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 96 time to evaluate : 1.160 Fit side-chains REVERT: A 488 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9175 (mt) REVERT: A 502 MET cc_start: 0.8880 (mmp) cc_final: 0.8465 (mmm) REVERT: B 488 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9140 (mt) REVERT: C 488 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9126 (mt) REVERT: C 502 MET cc_start: 0.9059 (mmm) cc_final: 0.7971 (mtm) REVERT: D 488 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9105 (mt) REVERT: D 502 MET cc_start: 0.8836 (mmp) cc_final: 0.8481 (mmm) outliers start: 33 outliers final: 21 residues processed: 118 average time/residue: 0.6637 time to fit residues: 92.3145 Evaluate side-chains 119 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 526 MET 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 287 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 526 MET 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 287 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 519 MET Chi-restraints excluded: chain C residue 526 MET 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 287 VAL Chi-restraints excluded: chain D residue 488 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 147 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 346 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 280 optimal weight: 1.9990 chunk 352 optimal weight: 0.2980 chunk 80 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 290 optimal weight: 5.9990 chunk 214 optimal weight: 5.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 ASN ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 836 ASN ** D 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.066463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.047851 restraints weight = 79702.725| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 3.15 r_work: 0.2582 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29116 Z= 0.147 Angle : 0.505 7.741 39600 Z= 0.260 Chirality : 0.041 0.171 4516 Planarity : 0.003 0.032 5016 Dihedral : 4.423 40.466 3884 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.28 % Allowed : 8.94 % Favored : 89.78 % 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 aren not related in a simple way. whole: 1.08 (0.15), residues: 3572 helix: 1.01 (0.13), residues: 1832 sheet: 0.12 (0.24), residues: 460 loop : 0.78 (0.19), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 706 TYR 0.012 0.001 TYR A 938 PHE 0.012 0.001 PHE A 107 TRP 0.013 0.001 TRP C 264 HIS 0.004 0.001 HIS B 354 Details of bonding type rmsd covalent geometry : bond 0.00340 (29116) covalent geometry : angle 0.50461 (39600) hydrogen bonds : bond 0.04155 ( 1480) hydrogen bonds : angle 4.27014 ( 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 137 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 98 time to evaluate : 1.168 Fit side-chains REVERT: A 502 MET cc_start: 0.8875 (mmp) cc_final: 0.8438 (mmm) REVERT: B 488 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9125 (mt) REVERT: B 713 MET cc_start: 0.9173 (mmt) cc_final: 0.8922 (mmt) REVERT: D 502 MET cc_start: 0.8829 (mmp) cc_final: 0.8479 (mmm) outliers start: 39 outliers final: 20 residues processed: 122 average time/residue: 0.7303 time to fit residues: 105.2096 Evaluate side-chains 113 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 526 MET 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 287 VAL Chi-restraints excluded: chain C residue 519 MET Chi-restraints excluded: chain C residue 526 MET 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 287 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 39 optimal weight: 2.9990 chunk 257 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 chunk 251 optimal weight: 2.9990 chunk 317 optimal weight: 3.9990 chunk 249 optimal weight: 3.9990 chunk 280 optimal weight: 3.9990 chunk 157 optimal weight: 0.5980 chunk 225 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 794 ASN ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 ASN ** 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 = 0.3207 r_free = 0.3207 target = 0.066550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.047873 restraints weight = 79276.808| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 3.10 r_work: 0.2576 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29116 Z= 0.144 Angle : 0.492 7.774 39600 Z= 0.253 Chirality : 0.040 0.168 4516 Planarity : 0.003 0.033 5016 Dihedral : 4.297 42.294 3884 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.51 % Allowed : 9.76 % 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 aren not related in a simple way. whole: 1.19 (0.15), residues: 3572 helix: 1.14 (0.13), residues: 1828 sheet: 0.06 (0.24), residues: 460 loop : 0.83 (0.18), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 706 TYR 0.012 0.001 TYR B 938 PHE 0.013 0.001 PHE B 107 TRP 0.011 0.001 TRP C 264 HIS 0.005 0.001 HIS C 354 Details of bonding type rmsd covalent geometry : bond 0.00332 (29116) covalent geometry : angle 0.49212 (39600) hydrogen bonds : bond 0.04071 ( 1480) hydrogen bonds : angle 4.20101 ( 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 138 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 92 time to evaluate : 1.100 Fit side-chains REVERT: A 508 THR cc_start: 0.8432 (OUTLIER) cc_final: 0.8090 (p) REVERT: A 713 MET cc_start: 0.9171 (mmt) cc_final: 0.8953 (mmt) REVERT: B 508 THR cc_start: 0.8423 (OUTLIER) cc_final: 0.8036 (p) REVERT: C 502 MET cc_start: 0.9110 (mmm) cc_final: 0.8836 (mmm) REVERT: C 508 THR cc_start: 0.8415 (OUTLIER) cc_final: 0.8025 (p) REVERT: D 502 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8565 (mmm) REVERT: D 508 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8019 (p) outliers start: 46 outliers final: 20 residues processed: 121 average time/residue: 0.5842 time to fit residues: 83.9768 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 : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 519 MET 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 287 VAL 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 287 VAL Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 519 MET Chi-restraints excluded: chain C residue 526 MET 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 287 VAL Chi-restraints excluded: chain D residue 502 MET 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: 6.9990 chunk 250 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 chunk 247 optimal weight: 3.9990 chunk 222 optimal weight: 4.9990 chunk 312 optimal weight: 0.0870 chunk 111 optimal weight: 7.9990 chunk 163 optimal weight: 10.0000 chunk 350 optimal weight: 5.9990 chunk 342 optimal weight: 10.0000 overall best weight: 2.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3207 r_free = 0.3207 target = 0.066512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.047776 restraints weight = 79383.631| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 3.12 r_work: 0.2572 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29116 Z= 0.144 Angle : 0.481 6.050 39600 Z= 0.249 Chirality : 0.040 0.169 4516 Planarity : 0.003 0.033 5016 Dihedral : 4.207 44.544 3884 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.31 % Allowed : 10.29 % Favored : 88.40 % 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 aren not related in a simple way. whole: 1.23 (0.15), residues: 3572 helix: 1.17 (0.13), residues: 1832 sheet: 0.05 (0.24), residues: 460 loop : 0.86 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 706 TYR 0.011 0.001 TYR A 938 PHE 0.013 0.001 PHE B 107 TRP 0.011 0.001 TRP A 264 HIS 0.003 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00334 (29116) covalent geometry : angle 0.48123 (39600) hydrogen bonds : bond 0.04011 ( 1480) hydrogen bonds : angle 4.14198 ( 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 137 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 97 time to evaluate : 1.008 Fit side-chains REVERT: A 496 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8929 (tpp) REVERT: A 508 THR cc_start: 0.8357 (OUTLIER) cc_final: 0.8012 (p) REVERT: B 502 MET cc_start: 0.8663 (mmt) cc_final: 0.8417 (mmm) REVERT: B 508 THR cc_start: 0.8349 (OUTLIER) cc_final: 0.7965 (p) REVERT: C 496 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8979 (tpp) REVERT: C 502 MET cc_start: 0.9069 (mmm) cc_final: 0.8807 (mmm) REVERT: C 508 THR cc_start: 0.8354 (OUTLIER) cc_final: 0.7959 (p) REVERT: D 502 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8543 (mmm) REVERT: D 508 THR cc_start: 0.8362 (OUTLIER) cc_final: 0.7956 (p) outliers start: 40 outliers final: 19 residues processed: 117 average time/residue: 0.6333 time to fit residues: 87.5053 Evaluate side-chains 120 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 519 MET 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 287 VAL 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 287 VAL Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 519 MET Chi-restraints excluded: chain C residue 526 MET 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 287 VAL Chi-restraints excluded: chain D residue 502 MET 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 1043 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 290 optimal weight: 5.9990 chunk 203 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 202 optimal weight: 0.7980 chunk 48 optimal weight: 9.9990 chunk 327 optimal weight: 9.9990 chunk 311 optimal weight: 1.9990 chunk 268 optimal weight: 0.2980 chunk 300 optimal weight: 6.9990 chunk 342 optimal weight: 0.0020 chunk 276 optimal weight: 9.9990 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 HIS ** D 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.068202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.050045 restraints weight = 79119.348| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 3.11 r_work: 0.2642 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29116 Z= 0.090 Angle : 0.454 7.901 39600 Z= 0.232 Chirality : 0.039 0.139 4516 Planarity : 0.003 0.033 5016 Dihedral : 4.003 43.194 3884 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.95 % Allowed : 10.65 % Favored : 88.40 % 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 aren not related in a simple way. whole: 1.42 (0.15), residues: 3572 helix: 1.32 (0.13), residues: 1824 sheet: -0.17 (0.23), residues: 504 loop : 1.14 (0.19), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 706 TYR 0.010 0.001 TYR C 938 PHE 0.012 0.001 PHE A 304 TRP 0.010 0.001 TRP B 514 HIS 0.003 0.000 HIS D 354 Details of bonding type rmsd covalent geometry : bond 0.00188 (29116) covalent geometry : angle 0.45432 (39600) hydrogen bonds : bond 0.03467 ( 1480) hydrogen bonds : angle 3.97649 ( 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 128 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 1.080 Fit side-chains REVERT: A 508 THR cc_start: 0.8414 (OUTLIER) cc_final: 0.7041 (p) REVERT: A 713 MET cc_start: 0.9152 (mmt) cc_final: 0.8903 (mmt) REVERT: B 502 MET cc_start: 0.8760 (mmt) cc_final: 0.8467 (mmm) REVERT: B 508 THR cc_start: 0.8372 (OUTLIER) cc_final: 0.6923 (p) REVERT: C 502 MET cc_start: 0.9000 (mmm) cc_final: 0.8580 (mmm) REVERT: C 508 THR cc_start: 0.8410 (OUTLIER) cc_final: 0.6911 (p) REVERT: D 508 THR cc_start: 0.8390 (OUTLIER) cc_final: 0.6956 (p) outliers start: 29 outliers final: 15 residues processed: 115 average time/residue: 0.5938 time to fit residues: 80.8557 Evaluate side-chains 115 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 508 THR Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 814 VAL 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 526 MET Chi-restraints excluded: chain B residue 814 VAL 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 814 VAL 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 814 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 31 optimal weight: 0.0970 chunk 157 optimal weight: 0.9990 chunk 168 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 190 optimal weight: 0.9990 chunk 355 optimal weight: 7.9990 chunk 254 optimal weight: 2.9990 chunk 332 optimal weight: 0.0050 chunk 46 optimal weight: 10.0000 chunk 347 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 HIS C 243 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.068725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.050626 restraints weight = 79415.565| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 3.10 r_work: 0.2657 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29116 Z= 0.087 Angle : 0.456 8.791 39600 Z= 0.231 Chirality : 0.038 0.140 4516 Planarity : 0.003 0.034 5016 Dihedral : 3.901 42.525 3884 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.79 % Allowed : 10.85 % Favored : 88.37 % 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 aren not related in a simple way. whole: 1.48 (0.15), residues: 3572 helix: 1.38 (0.13), residues: 1828 sheet: -0.08 (0.24), residues: 504 loop : 1.13 (0.19), residues: 1240 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 A 304 TRP 0.010 0.001 TRP D 514 HIS 0.002 0.000 HIS D 354 Details of bonding type rmsd covalent geometry : bond 0.00179 (29116) covalent geometry : angle 0.45574 (39600) hydrogen bonds : bond 0.03339 ( 1480) hydrogen bonds : angle 3.91070 ( 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 124 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 1.132 Fit side-chains REVERT: A 252 PHE cc_start: 0.9379 (OUTLIER) cc_final: 0.9050 (p90) REVERT: A 502 MET cc_start: 0.8706 (mmt) cc_final: 0.8445 (mmm) REVERT: A 511 MET cc_start: 0.8334 (mtm) cc_final: 0.8043 (mtm) REVERT: A 993 PHE cc_start: 0.9167 (t80) cc_final: 0.8881 (t80) REVERT: B 502 MET cc_start: 0.8731 (mmt) cc_final: 0.8484 (mmm) REVERT: B 511 MET cc_start: 0.8346 (mtm) cc_final: 0.8066 (mtm) REVERT: C 81 MET cc_start: 0.8447 (mmp) cc_final: 0.8244 (mmp) REVERT: C 502 MET cc_start: 0.9023 (mmm) cc_final: 0.8763 (mmm) REVERT: C 511 MET cc_start: 0.8364 (mtm) cc_final: 0.8080 (mtm) REVERT: D 81 MET cc_start: 0.8446 (mmp) cc_final: 0.8240 (mmp) REVERT: D 511 MET cc_start: 0.8371 (mtm) cc_final: 0.8085 (mtm) outliers start: 24 outliers final: 15 residues processed: 117 average time/residue: 0.6209 time to fit residues: 86.1241 Evaluate side-chains 113 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 519 MET Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 526 MET Chi-restraints excluded: chain B residue 814 VAL Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 526 MET Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 297 ILE 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: 0.9990 chunk 20 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 302 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 328 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 321 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3230 r_free = 0.3230 target = 0.067124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.048852 restraints weight = 79686.622| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 3.09 r_work: 0.2609 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29116 Z= 0.131 Angle : 0.483 9.171 39600 Z= 0.245 Chirality : 0.040 0.167 4516 Planarity : 0.003 0.034 5016 Dihedral : 3.983 45.340 3884 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.72 % Allowed : 10.98 % Favored : 88.30 % 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 aren not related in a simple way. whole: 1.44 (0.15), residues: 3572 helix: 1.35 (0.13), residues: 1836 sheet: 0.22 (0.25), residues: 464 loop : 0.91 (0.19), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 706 TYR 0.011 0.001 TYR C 938 PHE 0.014 0.001 PHE A 107 TRP 0.016 0.001 TRP B 80 HIS 0.003 0.001 HIS D 354 Details of bonding type rmsd covalent geometry : bond 0.00302 (29116) covalent geometry : angle 0.48267 (39600) hydrogen bonds : bond 0.03738 ( 1480) hydrogen bonds : angle 3.99089 ( 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: 22 poor density : 103 time to evaluate : 1.047 Fit side-chains REVERT: A 252 PHE cc_start: 0.9417 (OUTLIER) cc_final: 0.9101 (p90) REVERT: A 993 PHE cc_start: 0.9179 (t80) cc_final: 0.8890 (t80) REVERT: B 508 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.7923 (p) REVERT: B 511 MET cc_start: 0.8306 (mtm) cc_final: 0.8009 (mtm) REVERT: B 993 PHE cc_start: 0.9189 (t80) cc_final: 0.8898 (t80) REVERT: C 252 PHE cc_start: 0.9411 (OUTLIER) cc_final: 0.9132 (p90) REVERT: C 502 MET cc_start: 0.9054 (mmm) cc_final: 0.8671 (mmm) REVERT: C 508 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.7919 (p) REVERT: C 511 MET cc_start: 0.8320 (mtm) cc_final: 0.8007 (mtm) REVERT: C 993 PHE cc_start: 0.9186 (t80) cc_final: 0.8906 (t80) REVERT: D 252 PHE cc_start: 0.9413 (OUTLIER) cc_final: 0.9128 (p90) REVERT: D 508 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.7977 (p) REVERT: D 511 MET cc_start: 0.8321 (mtm) cc_final: 0.8065 (mtm) REVERT: D 993 PHE cc_start: 0.9180 (t80) cc_final: 0.8897 (t80) outliers start: 22 outliers final: 11 residues processed: 121 average time/residue: 0.5602 time to fit residues: 80.3237 Evaluate side-chains 117 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 519 MET Chi-restraints excluded: chain A residue 814 VAL Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 526 MET 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 508 THR Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 287 VAL 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 73 optimal weight: 1.9990 chunk 247 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 199 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 226 optimal weight: 0.4980 chunk 202 optimal weight: 1.9990 chunk 188 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 249 optimal weight: 8.9990 chunk 252 optimal weight: 0.0470 overall best weight: 0.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3257 r_free = 0.3257 target = 0.068391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.050275 restraints weight = 79317.078| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 3.09 r_work: 0.2647 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 29116 Z= 0.092 Angle : 0.469 9.657 39600 Z= 0.236 Chirality : 0.039 0.143 4516 Planarity : 0.003 0.034 5016 Dihedral : 3.910 45.196 3884 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.69 % Allowed : 11.07 % Favored : 88.24 % 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 aren not related in a simple way. whole: 1.51 (0.15), residues: 3572 helix: 1.44 (0.13), residues: 1828 sheet: -0.07 (0.24), residues: 508 loop : 1.08 (0.19), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 706 TYR 0.010 0.001 TYR C 938 PHE 0.012 0.001 PHE D 304 TRP 0.014 0.001 TRP A 80 HIS 0.002 0.000 HIS D 354 Details of bonding type rmsd covalent geometry : bond 0.00195 (29116) covalent geometry : angle 0.46878 (39600) hydrogen bonds : bond 0.03407 ( 1480) hydrogen bonds : angle 3.91367 ( 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 122 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 1.339 Fit side-chains REVERT: A 252 PHE cc_start: 0.9386 (OUTLIER) cc_final: 0.9095 (p90) REVERT: A 508 THR cc_start: 0.8426 (OUTLIER) cc_final: 0.8009 (p) REVERT: A 993 PHE cc_start: 0.9171 (t80) cc_final: 0.8881 (t80) REVERT: B 252 PHE cc_start: 0.9385 (OUTLIER) cc_final: 0.9095 (p90) REVERT: B 511 MET cc_start: 0.8379 (mtm) cc_final: 0.8065 (mtm) REVERT: B 993 PHE cc_start: 0.9176 (t80) cc_final: 0.8893 (t80) REVERT: C 252 PHE cc_start: 0.9381 (OUTLIER) cc_final: 0.9086 (p90) REVERT: C 496 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8938 (mmm) REVERT: C 502 MET cc_start: 0.9020 (mmm) cc_final: 0.8685 (mmm) REVERT: C 511 MET cc_start: 0.8350 (mtm) cc_final: 0.8079 (mtm) REVERT: C 993 PHE cc_start: 0.9162 (t80) cc_final: 0.8882 (t80) REVERT: D 252 PHE cc_start: 0.9383 (OUTLIER) cc_final: 0.9084 (p90) REVERT: D 496 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8905 (mmm) REVERT: D 511 MET cc_start: 0.8353 (mtm) cc_final: 0.8063 (mtm) REVERT: D 993 PHE cc_start: 0.9153 (t80) cc_final: 0.8871 (t80) outliers start: 21 outliers final: 14 residues processed: 118 average time/residue: 0.7276 time to fit residues: 101.9413 Evaluate side-chains 121 residues out of total 3152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 1.222 ------------------------------------------------------------------------------- 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 508 THR Chi-restraints excluded: chain A residue 519 MET 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 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 526 MET Chi-restraints excluded: chain C residue 814 VAL Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 496 MET 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: 2.9990 chunk 250 optimal weight: 20.0000 chunk 347 optimal weight: 1.9990 chunk 240 optimal weight: 10.0000 chunk 305 optimal weight: 10.0000 chunk 273 optimal weight: 20.0000 chunk 162 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 0.0770 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3235 r_free = 0.3235 target = 0.067362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.049061 restraints weight = 79781.922| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 3.12 r_work: 0.2613 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29116 Z= 0.124 Angle : 0.492 10.555 39600 Z= 0.246 Chirality : 0.040 0.163 4516 Planarity : 0.003 0.034 5016 Dihedral : 3.962 46.651 3884 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.79 % Allowed : 11.14 % Favored : 88.07 % 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 aren not related in a simple way. whole: 1.46 (0.15), residues: 3572 helix: 1.40 (0.13), residues: 1836 sheet: 0.17 (0.25), residues: 468 loop : 0.89 (0.19), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 706 TYR 0.011 0.001 TYR C 938 PHE 0.014 0.001 PHE A 304 TRP 0.008 0.001 TRP A 264 HIS 0.002 0.001 HIS C 354 Details of bonding type rmsd covalent geometry : bond 0.00288 (29116) covalent geometry : angle 0.49154 (39600) hydrogen bonds : bond 0.03648 ( 1480) hydrogen bonds : angle 3.95657 ( 3996) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5502.72 seconds wall clock time: 95 minutes 24.29 seconds (5724.29 seconds total)