Starting phenix.real_space_refine on Mon Aug 25 13:07:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9djv_46939/08_2025/9djv_46939.cif Found real_map, /net/cci-nas-00/data/ceres_data/9djv_46939/08_2025/9djv_46939.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9djv_46939/08_2025/9djv_46939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9djv_46939/08_2025/9djv_46939.map" model { file = "/net/cci-nas-00/data/ceres_data/9djv_46939/08_2025/9djv_46939.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9djv_46939/08_2025/9djv_46939.cif" } resolution = 3.4 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= 0.000 sd= 0.002 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 2 8.98 5 S 172 5.16 5 C 18328 2.51 5 N 4588 2.21 5 O 5116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 140 residue(s): 0.03s 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: 28206 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7051 Classifications: {'peptide': 899} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 35, 'TRANS': 863} Chain breaks: 5 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'ARG:plan': 7, 'ASN:plan1': 3, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 72 Chain: "B" Number of atoms: 7051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7051 Classifications: {'peptide': 899} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 35, 'TRANS': 863} Chain breaks: 5 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'ARG:plan': 7, 'ASN:plan1': 3, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 72 Chain: "C" Number of atoms: 7051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7051 Classifications: {'peptide': 899} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 35, 'TRANS': 863} Chain breaks: 5 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'ARG:plan': 7, 'ASN:plan1': 3, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 72 Chain: "D" Number of atoms: 7051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7051 Classifications: {'peptide': 899} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 35, 'TRANS': 863} Chain breaks: 5 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'ARG:plan': 7, 'ASN:plan1': 3, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 72 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.51, per 1000 atoms: 0.20 Number of scatterers: 28206 At special positions: 0 Unit cell: (145.631, 145.631, 123.308, 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 2 19.00 S 172 16.00 O 5116 8.00 N 4588 7.00 C 18328 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6784 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 24 sheets defined 59.3% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 15 through 44 removed outlier: 4.190A pdb=" N PHE A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.660A 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 123 removed outlier: 3.503A pdb=" N ILE A 111 " --> pdb=" O PHE A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 135 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 177 Processing helix chain 'A' and resid 178 through 188 removed outlier: 3.917A pdb=" N ILE A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 204 removed outlier: 3.704A 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: 4.737A pdb=" N GLY A 302 " --> pdb=" O MET A 298 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) Proline residue: A 309 - end of helix Processing helix chain 'A' and resid 341 through 353 removed outlier: 3.868A 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 454 through 460 removed outlier: 3.932A 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: 3.586A pdb=" N LEU A 488 " --> pdb=" O ALA A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 500 removed outlier: 3.612A pdb=" N LEU A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 3.768A 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: 3.673A pdb=" N VAL A 596 " --> pdb=" O SER A 592 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A 600 " --> pdb=" O VAL A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 721 through 726 removed outlier: 4.237A pdb=" N CYS A 725 " --> pdb=" O PRO A 721 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 769 through 773 Processing helix chain 'A' and resid 781 through 793 removed outlier: 3.656A pdb=" N ARG A 787 " --> pdb=" O ASP A 783 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS A 790 " --> pdb=" O HIS A 786 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N THR A 791 " --> pdb=" O ARG A 787 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 792 " --> pdb=" O GLU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 814 removed outlier: 3.616A pdb=" N LEU A 811 " --> pdb=" O ASN A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 819 Processing helix chain 'A' and resid 834 through 839 removed outlier: 3.752A pdb=" N VAL A 838 " --> pdb=" O ASP A 834 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASP A 839 " --> pdb=" O PRO A 835 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 834 through 839' Processing helix chain 'A' and resid 839 through 852 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: 3.617A 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 984 removed outlier: 3.571A pdb=" N ARG A 984 " --> pdb=" O ASN A 981 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 981 through 984' Processing helix chain 'A' and resid 997 through 1002 removed outlier: 3.574A 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: 4.190A pdb=" N PHE B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 3.661A 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 123 removed outlier: 3.504A pdb=" N ILE B 111 " --> pdb=" O PHE B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 135 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 177 Processing helix chain 'B' and resid 178 through 188 removed outlier: 3.917A pdb=" N ILE B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 204 removed outlier: 3.702A 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: 4.735A pdb=" N GLY B 302 " --> pdb=" O MET B 298 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) Proline residue: B 309 - end of helix Processing helix chain 'B' and resid 341 through 353 removed outlier: 3.868A 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 454 through 460 removed outlier: 3.931A 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: 3.586A pdb=" N LEU B 488 " --> pdb=" O ALA B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 500 removed outlier: 3.612A pdb=" N LEU B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 3.769A 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: 3.673A pdb=" N VAL B 596 " --> pdb=" O SER B 592 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG B 598 " --> pdb=" O GLU B 594 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA B 599 " --> pdb=" O GLU B 595 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE B 600 " --> pdb=" O VAL B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 616 Processing helix chain 'B' and resid 721 through 726 removed outlier: 4.237A pdb=" N CYS B 725 " --> pdb=" O PRO B 721 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 769 through 773 Processing helix chain 'B' and resid 781 through 793 removed outlier: 3.655A pdb=" N ARG B 787 " --> pdb=" O ASP B 783 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS B 790 " --> pdb=" O HIS B 786 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N THR B 791 " --> pdb=" O ARG B 787 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 792 " --> pdb=" O GLU B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 814 removed outlier: 3.510A pdb=" N LEU B 811 " --> pdb=" O ASN B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 819 Processing helix chain 'B' and resid 834 through 839 removed outlier: 3.752A pdb=" N VAL B 838 " --> pdb=" O ASP B 834 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASP B 839 " --> pdb=" O PRO B 835 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 834 through 839' Processing helix chain 'B' and resid 839 through 852 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: 3.618A 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 984 removed outlier: 3.571A pdb=" N ARG B 984 " --> pdb=" O ASN B 981 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 981 through 984' 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: 4.190A pdb=" N PHE C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) removed outlier: 3.661A 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 123 removed outlier: 3.502A pdb=" N ILE C 111 " --> pdb=" O PHE C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 135 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 177 Processing helix chain 'C' and resid 178 through 188 removed outlier: 3.918A pdb=" N ILE C 186 " --> pdb=" O SER C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 204 removed outlier: 3.704A 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: 4.736A pdb=" N GLY C 302 " --> pdb=" O MET C 298 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) Proline residue: C 309 - end of helix Processing helix chain 'C' and resid 341 through 353 removed outlier: 3.869A 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 454 through 460 removed outlier: 3.932A 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: 3.586A pdb=" N LEU C 488 " --> pdb=" O ALA C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 500 removed outlier: 3.613A pdb=" N LEU C 499 " --> pdb=" O LEU C 495 " (cutoff:3.500A) removed outlier: 3.768A 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: 3.674A pdb=" N VAL C 596 " --> pdb=" O SER C 592 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ARG C 598 " --> pdb=" O GLU C 594 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA C 599 " --> pdb=" O GLU C 595 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE C 600 " --> pdb=" O VAL C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 616 Processing helix chain 'C' and resid 721 through 726 removed outlier: 4.237A pdb=" N CYS C 725 " --> pdb=" O PRO C 721 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 769 through 773 Processing helix chain 'C' and resid 781 through 793 removed outlier: 3.656A pdb=" N ARG C 787 " --> pdb=" O ASP C 783 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS C 790 " --> pdb=" O HIS C 786 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N THR C 791 " --> pdb=" O ARG C 787 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 792 " --> pdb=" O GLU C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 814 removed outlier: 3.510A pdb=" N LEU C 811 " --> pdb=" O ASN C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 819 Processing helix chain 'C' and resid 834 through 839 removed outlier: 3.752A pdb=" N VAL C 838 " --> pdb=" O ASP C 834 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASP C 839 " --> pdb=" O PRO C 835 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 834 through 839' Processing helix chain 'C' and resid 839 through 852 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: 3.617A 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 984 removed outlier: 3.572A pdb=" N ARG C 984 " --> pdb=" O ASN C 981 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 981 through 984' Processing helix chain 'C' and resid 997 through 1002 removed outlier: 3.576A 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: 4.191A pdb=" N PHE D 19 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 3.660A 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 123 removed outlier: 3.503A pdb=" N ILE D 111 " --> pdb=" O PHE D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 135 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 177 Processing helix chain 'D' and resid 178 through 188 removed outlier: 3.917A pdb=" N ILE D 186 " --> pdb=" O SER D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 204 removed outlier: 3.704A 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: 4.736A pdb=" N GLY D 302 " --> pdb=" O MET D 298 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) Proline residue: D 309 - end of helix Processing helix chain 'D' and resid 341 through 353 removed outlier: 3.869A 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 454 through 460 removed outlier: 3.932A 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: 3.586A pdb=" N LEU D 488 " --> pdb=" O ALA D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 500 removed outlier: 3.612A pdb=" N LEU D 499 " --> pdb=" O LEU D 495 " (cutoff:3.500A) removed outlier: 3.768A 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: 3.673A pdb=" N VAL D 596 " --> pdb=" O SER D 592 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG D 598 " --> pdb=" O GLU D 594 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ALA D 599 " --> pdb=" O GLU D 595 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE D 600 " --> pdb=" O VAL D 596 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 616 Processing helix chain 'D' and resid 721 through 726 removed outlier: 4.237A pdb=" N CYS D 725 " --> pdb=" O PRO D 721 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 769 through 773 Processing helix chain 'D' and resid 781 through 793 removed outlier: 3.656A pdb=" N ARG D 787 " --> pdb=" O ASP D 783 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS D 790 " --> pdb=" O HIS D 786 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N THR D 791 " --> pdb=" O ARG D 787 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU D 792 " --> pdb=" O GLU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 807 through 814 removed outlier: 3.511A pdb=" N LEU D 811 " --> pdb=" O ASN D 807 " (cutoff:3.500A) Processing helix chain 'D' and resid 815 through 819 Processing helix chain 'D' and resid 834 through 839 removed outlier: 3.751A pdb=" N VAL D 838 " --> pdb=" O ASP D 834 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASP D 839 " --> pdb=" O PRO D 835 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 834 through 839' Processing helix chain 'D' and resid 839 through 852 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: 3.616A 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 984 removed outlier: 3.572A pdb=" N ARG D 984 " --> pdb=" O ASN D 981 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 981 through 984' Processing helix chain 'D' and resid 997 through 1002 removed outlier: 3.575A 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: 4.557A pdb=" N GLY A 338 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N HIS A 333 " --> pdb=" O ALA A 410 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N LEU A 412 " --> pdb=" O HIS A 333 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL A 335 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N LEU A 414 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 6.748A 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: 6.984A pdb=" N GLN A 585 " --> pdb=" O ILE A 558 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE A 558 " --> pdb=" O GLN A 585 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE A 587 " --> pdb=" O LEU A 556 " (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: 6.528A pdb=" N THR A 776 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU A 801 " --> pdb=" O THR A 776 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE A 778 " --> pdb=" O LEU A 801 " (cutoff:3.500A) removed outlier: 5.659A 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: 3.625A pdb=" N GLY A1023 " --> pdb=" O TYR A1060 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU A1062 " --> pdb=" O CYS A1021 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N CYS A1021 " --> pdb=" O LEU A1062 " (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: 4.557A pdb=" N GLY B 338 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N HIS B 333 " --> pdb=" O ALA B 410 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N LEU B 412 " --> pdb=" O HIS B 333 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 335 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N LEU B 414 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N CYS B 337 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL B 445 " --> pdb=" O ASP B 471 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL B 473 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL B 447 " --> pdb=" O VAL B 473 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 525 through 530 removed outlier: 6.984A pdb=" N GLN B 585 " --> pdb=" O ILE B 558 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE B 558 " --> pdb=" O GLN B 585 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N PHE B 587 " --> pdb=" O LEU B 556 " (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: 6.529A pdb=" N THR B 776 " --> pdb=" O SER B 799 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU B 801 " --> pdb=" O THR B 776 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE B 778 " --> pdb=" O LEU B 801 " (cutoff:3.500A) removed outlier: 5.660A 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: 3.624A pdb=" N GLY B1023 " --> pdb=" O TYR B1060 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU B1062 " --> pdb=" O CYS B1021 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N CYS B1021 " --> pdb=" O LEU B1062 " (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: 4.557A pdb=" N GLY C 338 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N HIS C 333 " --> pdb=" O ALA C 410 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N LEU C 412 " --> pdb=" O HIS C 333 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL C 335 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N LEU C 414 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N CYS C 337 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL C 445 " --> pdb=" O ASP C 471 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL C 473 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL C 447 " --> pdb=" O VAL C 473 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 525 through 530 removed outlier: 6.984A pdb=" N GLN C 585 " --> pdb=" O ILE C 558 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE C 558 " --> pdb=" O GLN C 585 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE C 587 " --> pdb=" O LEU C 556 " (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: 6.528A pdb=" N THR C 776 " --> pdb=" O SER C 799 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU C 801 " --> pdb=" O THR C 776 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE C 778 " --> pdb=" O LEU C 801 " (cutoff:3.500A) removed outlier: 5.660A 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: 3.624A pdb=" N GLY C1023 " --> pdb=" O TYR C1060 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU C1062 " --> pdb=" O CYS C1021 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N CYS C1021 " --> pdb=" O LEU C1062 " (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: 4.558A pdb=" N GLY D 338 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N HIS D 333 " --> pdb=" O ALA D 410 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N LEU D 412 " --> pdb=" O HIS D 333 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL D 335 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N LEU D 414 " --> pdb=" O VAL D 335 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N CYS D 337 " --> pdb=" O LEU D 414 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL D 445 " --> pdb=" O ASP D 471 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL D 473 " --> pdb=" O VAL D 445 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL D 447 " --> pdb=" O VAL D 473 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 525 through 530 removed outlier: 6.984A pdb=" N GLN D 585 " --> pdb=" O ILE D 558 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE D 558 " --> pdb=" O GLN D 585 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N PHE D 587 " --> pdb=" O LEU D 556 " (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: 6.528A pdb=" N THR D 776 " --> pdb=" O SER D 799 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N LEU D 801 " --> pdb=" O THR D 776 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE D 778 " --> pdb=" O LEU D 801 " (cutoff:3.500A) removed outlier: 5.659A 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: 3.624A pdb=" N GLY D1023 " --> pdb=" O TYR D1060 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU D1062 " --> pdb=" O CYS D1021 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N CYS D1021 " --> pdb=" O LEU D1062 " (cutoff:3.500A) 1500 hydrogen bonds defined for protein. 4041 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: 5.20 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5459 1.32 - 1.45: 7235 1.45 - 1.57: 15934 1.57 - 1.70: 0 1.70 - 1.82: 260 Bond restraints: 28888 Sorted by residual: bond pdb=" CA PRO D1047 " pdb=" C PRO D1047 " ideal model delta sigma weight residual 1.514 1.541 -0.026 5.50e-03 3.31e+04 2.30e+01 bond pdb=" CA PRO A1047 " pdb=" C PRO A1047 " ideal model delta sigma weight residual 1.514 1.540 -0.025 5.50e-03 3.31e+04 2.12e+01 bond pdb=" CA PRO C1047 " pdb=" C PRO C1047 " ideal model delta sigma weight residual 1.514 1.539 -0.025 5.50e-03 3.31e+04 2.08e+01 bond pdb=" CA PRO B1047 " pdb=" C PRO B1047 " ideal model delta sigma weight residual 1.514 1.539 -0.025 5.50e-03 3.31e+04 2.08e+01 bond pdb=" CA ARG C 986 " pdb=" C ARG C 986 " ideal model delta sigma weight residual 1.522 1.479 0.043 1.21e-02 6.83e+03 1.25e+01 ... (remaining 28883 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 25818 1.50 - 3.00: 10671 3.00 - 4.50: 2407 4.50 - 6.00: 360 6.00 - 7.50: 44 Bond angle restraints: 39300 Sorted by residual: angle pdb=" CA ASN A 940 " pdb=" CB ASN A 940 " pdb=" CG ASN A 940 " ideal model delta sigma weight residual 112.60 118.26 -5.66 1.00e+00 1.00e+00 3.20e+01 angle pdb=" CA ASN B 940 " pdb=" CB ASN B 940 " pdb=" CG ASN B 940 " ideal model delta sigma weight residual 112.60 118.24 -5.64 1.00e+00 1.00e+00 3.18e+01 angle pdb=" CA ASN C 940 " pdb=" CB ASN C 940 " pdb=" CG ASN C 940 " ideal model delta sigma weight residual 112.60 118.24 -5.64 1.00e+00 1.00e+00 3.18e+01 angle pdb=" CA ASN D 940 " pdb=" CB ASN D 940 " pdb=" CG ASN D 940 " ideal model delta sigma weight residual 112.60 118.21 -5.61 1.00e+00 1.00e+00 3.15e+01 angle pdb=" CA ASP C 895 " pdb=" CB ASP C 895 " pdb=" CG ASP C 895 " ideal model delta sigma weight residual 112.60 117.96 -5.36 1.00e+00 1.00e+00 2.87e+01 ... (remaining 39295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 15760 17.27 - 34.54: 945 34.54 - 51.80: 139 51.80 - 69.07: 44 69.07 - 86.34: 36 Dihedral angle restraints: 16924 sinusoidal: 6432 harmonic: 10492 Sorted by residual: dihedral pdb=" CA TYR B 212 " pdb=" C TYR B 212 " pdb=" N LEU B 213 " pdb=" CA LEU B 213 " ideal model delta harmonic sigma weight residual 180.00 152.21 27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA TYR C 212 " pdb=" C TYR C 212 " pdb=" N LEU C 213 " pdb=" CA LEU C 213 " ideal model delta harmonic sigma weight residual 180.00 152.22 27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA TYR A 212 " pdb=" C TYR A 212 " pdb=" N LEU A 213 " pdb=" CA LEU A 213 " ideal model delta harmonic sigma weight residual 180.00 152.23 27.77 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 16921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2877 0.083 - 0.166: 1351 0.166 - 0.249: 223 0.249 - 0.332: 37 0.332 - 0.415: 8 Chirality restraints: 4496 Sorted by residual: chirality pdb=" CA PRO A 490 " pdb=" N PRO A 490 " pdb=" C PRO A 490 " pdb=" CB PRO A 490 " both_signs ideal model delta sigma weight residual False 2.72 2.30 0.41 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" CA PRO D 490 " pdb=" N PRO D 490 " pdb=" C PRO D 490 " pdb=" CB PRO D 490 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CA PRO C 490 " pdb=" N PRO C 490 " pdb=" C PRO C 490 " pdb=" CB PRO C 490 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.41 2.00e-01 2.50e+01 4.20e+00 ... (remaining 4493 not shown) Planarity restraints: 4968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B1060 " 0.105 2.00e-02 2.50e+03 6.57e-02 8.63e+01 pdb=" CG TYR B1060 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR B1060 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR B1060 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR B1060 " -0.052 2.00e-02 2.50e+03 pdb=" CE2 TYR B1060 " -0.049 2.00e-02 2.50e+03 pdb=" CZ TYR B1060 " -0.019 2.00e-02 2.50e+03 pdb=" OH TYR B1060 " 0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1060 " 0.105 2.00e-02 2.50e+03 6.55e-02 8.58e+01 pdb=" CG TYR A1060 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR A1060 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR A1060 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR A1060 " -0.052 2.00e-02 2.50e+03 pdb=" CE2 TYR A1060 " -0.049 2.00e-02 2.50e+03 pdb=" CZ TYR A1060 " -0.019 2.00e-02 2.50e+03 pdb=" OH TYR A1060 " 0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D1060 " 0.105 2.00e-02 2.50e+03 6.55e-02 8.58e+01 pdb=" CG TYR D1060 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR D1060 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR D1060 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR D1060 " -0.052 2.00e-02 2.50e+03 pdb=" CE2 TYR D1060 " -0.049 2.00e-02 2.50e+03 pdb=" CZ TYR D1060 " -0.019 2.00e-02 2.50e+03 pdb=" OH TYR D1060 " 0.117 2.00e-02 2.50e+03 ... (remaining 4965 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.85: 8644 2.85 - 3.42: 33428 3.42 - 3.99: 54705 3.99 - 4.57: 74834 4.57 - 5.14: 111609 Nonbonded interactions: 283220 Sorted by model distance: nonbonded pdb=" OD1 ASN B 460 " pdb=" NH1 ARG C 808 " model vdw 2.276 3.120 nonbonded pdb=" OD1 ASN A 460 " pdb=" NH1 ARG B 808 " model vdw 2.307 3.120 nonbonded pdb=" OD1 ASN C 460 " pdb=" NH1 ARG D 808 " model vdw 2.311 3.120 nonbonded pdb=" CD2 LEU A 837 " pdb=" NE2 GLN D 424 " model vdw 2.377 3.540 nonbonded pdb=" O ARG A 808 " pdb=" C ALA A 809 " model vdw 2.392 3.270 ... (remaining 283215 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 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: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 23.890 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.046 28888 Z= 0.690 Angle : 1.651 7.499 39300 Z= 1.104 Chirality : 0.091 0.415 4496 Planarity : 0.012 0.102 4968 Dihedral : 12.850 86.338 10140 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.66 % Allowed : 3.58 % Favored : 95.76 % 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: -0.95 (0.13), residues: 3548 helix: -0.85 (0.11), residues: 1788 sheet: 0.28 (0.27), residues: 348 loop : -0.30 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 503 TYR 0.117 0.017 TYR B1060 PHE 0.063 0.011 PHE D 587 TRP 0.106 0.023 TRP D 167 HIS 0.013 0.003 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.01160 (28888) covalent geometry : angle 1.65060 (39300) hydrogen bonds : bond 0.15222 ( 1500) hydrogen bonds : angle 7.36857 ( 4041) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.899 Fit side-chains REVERT: A 713 MET cc_start: 0.9049 (mmt) cc_final: 0.8549 (mmt) REVERT: A 891 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8533 (tm-30) REVERT: A 915 MET cc_start: 0.9233 (mmm) cc_final: 0.8969 (mmm) REVERT: B 713 MET cc_start: 0.8998 (mmt) cc_final: 0.8552 (mmt) REVERT: B 891 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8434 (tm-30) REVERT: B 915 MET cc_start: 0.9151 (mmm) cc_final: 0.8851 (mmm) REVERT: C 713 MET cc_start: 0.9023 (mmt) cc_final: 0.8621 (mmt) REVERT: C 891 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.8375 (tm-30) REVERT: C 915 MET cc_start: 0.9169 (mmm) cc_final: 0.8888 (mmm) REVERT: D 395 MET cc_start: 0.9326 (mmm) cc_final: 0.9112 (mmt) REVERT: D 713 MET cc_start: 0.8957 (mmt) cc_final: 0.8539 (mmt) REVERT: D 891 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8435 (tm-30) REVERT: D 915 MET cc_start: 0.9137 (mmm) cc_final: 0.8861 (mmm) outliers start: 20 outliers final: 4 residues processed: 112 average time/residue: 0.1501 time to fit residues: 30.1050 Evaluate side-chains 100 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 891 GLU Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain B residue 891 GLU Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain C residue 891 GLU Chi-restraints excluded: chain C residue 895 ASP Chi-restraints excluded: chain D residue 891 GLU Chi-restraints excluded: chain D residue 895 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN A 398 ASN A 894 ASN A 989 GLN A1046 ASN B 347 ASN B 398 ASN B 894 ASN B 989 GLN B1046 ASN C 347 ASN C 398 ASN C 894 ASN C 989 GLN C1046 ASN D 347 ASN D 398 ASN D 894 ASN D 989 GLN D1046 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.049020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.038047 restraints weight = 145816.850| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 4.09 r_work: 0.2676 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28888 Z= 0.129 Angle : 0.575 6.465 39300 Z= 0.303 Chirality : 0.043 0.156 4496 Planarity : 0.004 0.041 4968 Dihedral : 5.731 58.773 3868 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.60 % Allowed : 5.17 % Favored : 94.23 % 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: 0.67 (0.14), residues: 3548 helix: 0.66 (0.12), residues: 1812 sheet: -0.04 (0.24), residues: 476 loop : 0.61 (0.19), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 757 TYR 0.015 0.001 TYR D 452 PHE 0.011 0.001 PHE B1027 TRP 0.019 0.002 TRP B 514 HIS 0.003 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00271 (28888) covalent geometry : angle 0.57477 (39300) hydrogen bonds : bond 0.04600 ( 1500) hydrogen bonds : angle 4.87635 ( 4041) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 1.026 Fit side-chains REVERT: A 519 MET cc_start: 0.9460 (OUTLIER) cc_final: 0.9178 (tpt) REVERT: B 496 MET cc_start: 0.9449 (tpt) cc_final: 0.9068 (tpt) REVERT: B 519 MET cc_start: 0.9449 (OUTLIER) cc_final: 0.9194 (tpt) REVERT: C 519 MET cc_start: 0.9450 (OUTLIER) cc_final: 0.9187 (tpt) REVERT: D 395 MET cc_start: 0.9331 (mmm) cc_final: 0.9007 (mmt) REVERT: D 496 MET cc_start: 0.9458 (tpt) cc_final: 0.9071 (tpt) REVERT: D 519 MET cc_start: 0.9441 (OUTLIER) cc_final: 0.9190 (tpt) outliers start: 18 outliers final: 12 residues processed: 104 average time/residue: 0.1599 time to fit residues: 29.5656 Evaluate side-chains 108 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 519 MET Chi-restraints excluded: chain C residue 947 ILE Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 519 MET Chi-restraints excluded: chain D residue 947 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 291 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 131 optimal weight: 20.0000 chunk 269 optimal weight: 20.0000 chunk 90 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 45 optimal weight: 0.5980 chunk 187 optimal weight: 10.0000 chunk 311 optimal weight: 0.0870 chunk 325 optimal weight: 20.0000 chunk 143 optimal weight: 20.0000 overall best weight: 3.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN B 15 GLN B 836 ASN C 15 GLN C 836 ASN C1046 ASN D 15 GLN D 836 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.048536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.037584 restraints weight = 147234.003| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 4.11 r_work: 0.2659 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28888 Z= 0.147 Angle : 0.505 5.373 39300 Z= 0.262 Chirality : 0.040 0.152 4496 Planarity : 0.003 0.040 4968 Dihedral : 4.669 49.909 3848 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.80 % Allowed : 6.03 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.15), residues: 3548 helix: 1.04 (0.13), residues: 1808 sheet: 0.02 (0.24), residues: 480 loop : 0.99 (0.19), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 986 TYR 0.010 0.001 TYR A 938 PHE 0.011 0.001 PHE D1000 TRP 0.013 0.001 TRP B 514 HIS 0.003 0.001 HIS C 368 Details of bonding type rmsd covalent geometry : bond 0.00332 (28888) covalent geometry : angle 0.50490 (39300) hydrogen bonds : bond 0.03956 ( 1500) hydrogen bonds : angle 4.46350 ( 4041) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.990 Fit side-chains REVERT: A 496 MET cc_start: 0.9536 (tpt) cc_final: 0.9266 (tpt) REVERT: A 713 MET cc_start: 0.9349 (mmt) cc_final: 0.8644 (mmm) REVERT: A 832 MET cc_start: 0.9009 (ptt) cc_final: 0.8759 (ptt) REVERT: A 915 MET cc_start: 0.9345 (mmm) cc_final: 0.9002 (mmm) REVERT: B 519 MET cc_start: 0.9490 (OUTLIER) cc_final: 0.9255 (tpt) REVERT: B 713 MET cc_start: 0.9350 (mmt) cc_final: 0.8678 (mmm) REVERT: B 832 MET cc_start: 0.8993 (ptt) cc_final: 0.8777 (ptt) REVERT: C 496 MET cc_start: 0.9490 (tpt) cc_final: 0.9250 (tpt) REVERT: C 519 MET cc_start: 0.9498 (OUTLIER) cc_final: 0.9245 (tpt) REVERT: C 713 MET cc_start: 0.9353 (mmt) cc_final: 0.8675 (mmm) REVERT: C 832 MET cc_start: 0.9049 (ptt) cc_final: 0.8829 (ptt) REVERT: D 395 MET cc_start: 0.9341 (mmm) cc_final: 0.8935 (mmt) REVERT: D 519 MET cc_start: 0.9501 (OUTLIER) cc_final: 0.9242 (tpt) REVERT: D 713 MET cc_start: 0.9365 (mmt) cc_final: 0.8696 (mmm) REVERT: D 832 MET cc_start: 0.8967 (ptt) cc_final: 0.8728 (ptt) outliers start: 24 outliers final: 8 residues processed: 112 average time/residue: 0.1515 time to fit residues: 29.9394 Evaluate side-chains 103 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 519 MET Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 519 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 204 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 285 optimal weight: 0.9980 chunk 192 optimal weight: 20.0000 chunk 345 optimal weight: 1.9990 chunk 237 optimal weight: 10.0000 chunk 238 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 328 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.048928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.037978 restraints weight = 146259.141| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 4.07 r_work: 0.2678 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 28888 Z= 0.111 Angle : 0.471 8.660 39300 Z= 0.242 Chirality : 0.039 0.139 4496 Planarity : 0.003 0.041 4968 Dihedral : 4.347 42.910 3848 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.93 % Allowed : 6.27 % Favored : 92.81 % 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: 1.40 (0.15), residues: 3548 helix: 1.21 (0.13), residues: 1812 sheet: 0.22 (0.25), residues: 456 loop : 1.07 (0.19), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 432 TYR 0.018 0.001 TYR A 914 PHE 0.009 0.001 PHE D1000 TRP 0.013 0.001 TRP A 514 HIS 0.002 0.000 HIS C 368 Details of bonding type rmsd covalent geometry : bond 0.00246 (28888) covalent geometry : angle 0.47129 (39300) hydrogen bonds : bond 0.03554 ( 1500) hydrogen bonds : angle 4.24944 ( 4041) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.732 Fit side-chains REVERT: A 496 MET cc_start: 0.9468 (tpt) cc_final: 0.9169 (tpt) REVERT: A 519 MET cc_start: 0.9643 (tpt) cc_final: 0.9172 (tmm) REVERT: A 832 MET cc_start: 0.9005 (ptt) cc_final: 0.8725 (ptt) REVERT: B 496 MET cc_start: 0.9409 (tpt) cc_final: 0.9183 (tpt) REVERT: B 519 MET cc_start: 0.9502 (OUTLIER) cc_final: 0.9244 (tpt) REVERT: B 713 MET cc_start: 0.9309 (mmt) cc_final: 0.8549 (mmm) REVERT: B 832 MET cc_start: 0.8983 (ptt) cc_final: 0.8708 (ptt) REVERT: C 496 MET cc_start: 0.9411 (tpt) cc_final: 0.9132 (tpt) REVERT: C 519 MET cc_start: 0.9499 (OUTLIER) cc_final: 0.9218 (tpt) REVERT: C 713 MET cc_start: 0.9316 (mmt) cc_final: 0.8839 (mmt) REVERT: C 832 MET cc_start: 0.9003 (ptt) cc_final: 0.8741 (ptt) REVERT: D 496 MET cc_start: 0.9412 (tpt) cc_final: 0.9185 (tpt) REVERT: D 519 MET cc_start: 0.9493 (OUTLIER) cc_final: 0.9227 (tpt) REVERT: D 524 MET cc_start: 0.9012 (mmm) cc_final: 0.8675 (mmm) REVERT: D 713 MET cc_start: 0.9317 (mmt) cc_final: 0.8843 (mmt) REVERT: D 832 MET cc_start: 0.8969 (ptt) cc_final: 0.8716 (ptt) REVERT: D 837 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9165 (tt) outliers start: 28 outliers final: 8 residues processed: 117 average time/residue: 0.1581 time to fit residues: 32.6703 Evaluate side-chains 104 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 519 MET Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 519 MET Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 519 MET Chi-restraints excluded: chain D residue 837 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 65 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 59 optimal weight: 0.0010 chunk 209 optimal weight: 9.9990 chunk 299 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 88 optimal weight: 0.0020 chunk 117 optimal weight: 9.9990 chunk 250 optimal weight: 6.9990 chunk 329 optimal weight: 4.9990 overall best weight: 2.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.048731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.037600 restraints weight = 145926.319| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 4.11 r_work: 0.2669 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28888 Z= 0.123 Angle : 0.467 12.966 39300 Z= 0.240 Chirality : 0.039 0.140 4496 Planarity : 0.003 0.042 4968 Dihedral : 4.149 37.010 3848 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.80 % Allowed : 6.76 % Favored : 92.44 % 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: 1.45 (0.15), residues: 3548 helix: 1.23 (0.13), residues: 1812 sheet: 0.20 (0.25), residues: 464 loop : 1.16 (0.19), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 432 TYR 0.011 0.001 TYR C 938 PHE 0.009 0.001 PHE D1000 TRP 0.011 0.001 TRP D 514 HIS 0.002 0.001 HIS C 368 Details of bonding type rmsd covalent geometry : bond 0.00278 (28888) covalent geometry : angle 0.46667 (39300) hydrogen bonds : bond 0.03476 ( 1500) hydrogen bonds : angle 4.17135 ( 4041) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 1.005 Fit side-chains REVERT: A 713 MET cc_start: 0.9248 (mmt) cc_final: 0.8655 (mmm) REVERT: A 832 MET cc_start: 0.9012 (ptt) cc_final: 0.8739 (ptt) REVERT: B 496 MET cc_start: 0.9400 (tpt) cc_final: 0.9143 (tpt) REVERT: B 713 MET cc_start: 0.9285 (mmt) cc_final: 0.8505 (mmm) REVERT: B 832 MET cc_start: 0.9014 (ptt) cc_final: 0.8765 (ptt) REVERT: B 837 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9180 (tt) REVERT: B 915 MET cc_start: 0.9335 (mmm) cc_final: 0.9041 (mmm) REVERT: C 519 MET cc_start: 0.9508 (OUTLIER) cc_final: 0.9219 (tpt) REVERT: C 713 MET cc_start: 0.9291 (mmt) cc_final: 0.8813 (mmt) REVERT: C 832 MET cc_start: 0.9022 (ptt) cc_final: 0.8773 (ptt) REVERT: C 837 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9212 (tt) REVERT: D 496 MET cc_start: 0.9394 (tpt) cc_final: 0.9134 (tpt) REVERT: D 713 MET cc_start: 0.9290 (mmt) cc_final: 0.8814 (mmt) REVERT: D 832 MET cc_start: 0.8995 (ptt) cc_final: 0.8701 (ptt) REVERT: D 837 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9192 (tt) REVERT: D 915 MET cc_start: 0.9318 (mmm) cc_final: 0.9010 (mmm) outliers start: 24 outliers final: 8 residues processed: 114 average time/residue: 0.1387 time to fit residues: 28.1970 Evaluate side-chains 106 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 519 MET Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 837 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 282 optimal weight: 6.9990 chunk 309 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 153 optimal weight: 8.9990 chunk 76 optimal weight: 0.0770 chunk 351 optimal weight: 10.0000 chunk 189 optimal weight: 8.9990 chunk 111 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 81 optimal weight: 0.0070 overall best weight: 1.8158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 ASN D1046 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.049063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.037921 restraints weight = 145672.962| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 4.13 r_work: 0.2678 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28888 Z= 0.100 Angle : 0.465 13.928 39300 Z= 0.236 Chirality : 0.039 0.139 4496 Planarity : 0.003 0.043 4968 Dihedral : 4.040 32.235 3848 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.70 % Allowed : 7.06 % Favored : 92.24 % 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: 1.56 (0.15), residues: 3548 helix: 1.28 (0.13), residues: 1816 sheet: 0.26 (0.25), residues: 484 loop : 1.29 (0.19), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 503 TYR 0.017 0.001 TYR D 914 PHE 0.012 0.001 PHE A1010 TRP 0.012 0.001 TRP D 514 HIS 0.002 0.000 HIS D 368 Details of bonding type rmsd covalent geometry : bond 0.00219 (28888) covalent geometry : angle 0.46511 (39300) hydrogen bonds : bond 0.03348 ( 1500) hydrogen bonds : angle 4.10024 ( 4041) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 1.110 Fit side-chains REVERT: A 713 MET cc_start: 0.9240 (mmt) cc_final: 0.8529 (mmm) REVERT: A 832 MET cc_start: 0.8980 (ptt) cc_final: 0.8703 (ptt) REVERT: B 496 MET cc_start: 0.9430 (tpt) cc_final: 0.9129 (tpt) REVERT: B 713 MET cc_start: 0.9283 (mmt) cc_final: 0.8822 (mmt) REVERT: B 832 MET cc_start: 0.8991 (ptt) cc_final: 0.8741 (ptt) REVERT: B 837 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9217 (tt) REVERT: C 519 MET cc_start: 0.9516 (OUTLIER) cc_final: 0.9303 (tpt) REVERT: C 713 MET cc_start: 0.9280 (mmt) cc_final: 0.8816 (mmt) REVERT: C 832 MET cc_start: 0.8965 (ptt) cc_final: 0.8718 (ptt) REVERT: C 837 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9217 (tt) REVERT: C 915 MET cc_start: 0.9317 (mmm) cc_final: 0.9014 (mmm) REVERT: D 496 MET cc_start: 0.9423 (tpt) cc_final: 0.9121 (tpt) REVERT: D 713 MET cc_start: 0.9287 (mmt) cc_final: 0.8822 (mmt) REVERT: D 832 MET cc_start: 0.8964 (ptt) cc_final: 0.8666 (ptt) REVERT: D 837 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9230 (tt) outliers start: 21 outliers final: 11 residues processed: 114 average time/residue: 0.1322 time to fit residues: 26.7806 Evaluate side-chains 107 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 519 MET Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 274 MET Chi-restraints excluded: chain D residue 837 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 234 optimal weight: 8.9990 chunk 87 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 297 optimal weight: 9.9990 chunk 60 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 176 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 334 optimal weight: 2.9990 chunk 293 optimal weight: 8.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.047971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.036832 restraints weight = 146335.846| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 4.10 r_work: 0.2638 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28888 Z= 0.180 Angle : 0.504 10.948 39300 Z= 0.255 Chirality : 0.040 0.151 4496 Planarity : 0.003 0.041 4968 Dihedral : 4.006 26.097 3848 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.60 % Allowed : 7.69 % Favored : 91.71 % 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: 1.54 (0.15), residues: 3548 helix: 1.29 (0.13), residues: 1816 sheet: 0.27 (0.25), residues: 484 loop : 1.23 (0.19), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 948 TYR 0.011 0.001 TYR D 938 PHE 0.011 0.001 PHE B 492 TRP 0.012 0.001 TRP D 514 HIS 0.003 0.001 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00407 (28888) covalent geometry : angle 0.50421 (39300) hydrogen bonds : bond 0.03527 ( 1500) hydrogen bonds : angle 4.15261 ( 4041) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.903 Fit side-chains REVERT: A 496 MET cc_start: 0.9414 (tpt) cc_final: 0.9116 (tpt) REVERT: A 511 MET cc_start: 0.8760 (ptp) cc_final: 0.8492 (ptp) REVERT: A 713 MET cc_start: 0.9278 (mmt) cc_final: 0.8653 (mmm) REVERT: A 832 MET cc_start: 0.8959 (ptt) cc_final: 0.8712 (ptt) REVERT: A 837 LEU cc_start: 0.9556 (OUTLIER) cc_final: 0.9308 (tt) REVERT: B 496 MET cc_start: 0.9475 (tpt) cc_final: 0.9188 (tpt) REVERT: B 713 MET cc_start: 0.9306 (mmt) cc_final: 0.8933 (mmt) REVERT: B 832 MET cc_start: 0.8998 (ptt) cc_final: 0.8744 (ptt) REVERT: B 837 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9246 (tt) REVERT: C 496 MET cc_start: 0.9399 (tpt) cc_final: 0.9113 (tpt) REVERT: C 511 MET cc_start: 0.8764 (ptp) cc_final: 0.8509 (ptp) REVERT: C 519 MET cc_start: 0.9526 (OUTLIER) cc_final: 0.9303 (tpt) REVERT: C 713 MET cc_start: 0.9294 (mmt) cc_final: 0.8810 (mmt) REVERT: C 832 MET cc_start: 0.8995 (ptt) cc_final: 0.8736 (ptt) REVERT: C 837 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9317 (tt) REVERT: C 915 MET cc_start: 0.9357 (mmm) cc_final: 0.9040 (mmm) REVERT: D 496 MET cc_start: 0.9464 (tpt) cc_final: 0.9165 (tpt) REVERT: D 713 MET cc_start: 0.9301 (mmt) cc_final: 0.8817 (mmt) outliers start: 18 outliers final: 13 residues processed: 108 average time/residue: 0.1574 time to fit residues: 30.0647 Evaluate side-chains 109 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 519 MET Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 274 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 109 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 315 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 223 optimal weight: 9.9990 chunk 205 optimal weight: 8.9990 chunk 261 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 232 optimal weight: 10.0000 chunk 335 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.047793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.036636 restraints weight = 147711.135| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 4.10 r_work: 0.2632 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28888 Z= 0.179 Angle : 0.499 11.631 39300 Z= 0.252 Chirality : 0.040 0.149 4496 Planarity : 0.003 0.042 4968 Dihedral : 3.950 19.436 3848 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.63 % Allowed : 7.99 % Favored : 91.38 % 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: 1.53 (0.15), residues: 3548 helix: 1.30 (0.13), residues: 1816 sheet: 0.23 (0.25), residues: 484 loop : 1.19 (0.19), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 808 TYR 0.011 0.001 TYR C 938 PHE 0.010 0.001 PHE A 292 TRP 0.014 0.001 TRP D 514 HIS 0.003 0.001 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.00408 (28888) covalent geometry : angle 0.49921 (39300) hydrogen bonds : bond 0.03515 ( 1500) hydrogen bonds : angle 4.14799 ( 4041) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.825 Fit side-chains REVERT: A 511 MET cc_start: 0.8814 (ptp) cc_final: 0.8495 (ptp) REVERT: A 713 MET cc_start: 0.9289 (mmt) cc_final: 0.8674 (mmm) REVERT: A 837 LEU cc_start: 0.9583 (OUTLIER) cc_final: 0.9352 (tt) REVERT: B 496 MET cc_start: 0.9502 (tpt) cc_final: 0.9194 (tpt) REVERT: B 713 MET cc_start: 0.9311 (mmt) cc_final: 0.8943 (mmt) REVERT: B 837 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9339 (tt) REVERT: C 511 MET cc_start: 0.8833 (ptp) cc_final: 0.8524 (ptp) REVERT: C 519 MET cc_start: 0.9528 (OUTLIER) cc_final: 0.9305 (tpt) REVERT: C 713 MET cc_start: 0.9304 (mmt) cc_final: 0.8935 (mmt) REVERT: C 837 LEU cc_start: 0.9564 (OUTLIER) cc_final: 0.9342 (tt) REVERT: C 915 MET cc_start: 0.9349 (mmm) cc_final: 0.9006 (mmm) REVERT: D 496 MET cc_start: 0.9502 (tpt) cc_final: 0.9171 (tpt) REVERT: D 519 MET cc_start: 0.9593 (mmm) cc_final: 0.8907 (tmm) REVERT: D 713 MET cc_start: 0.9310 (mmt) cc_final: 0.8940 (mmt) outliers start: 19 outliers final: 13 residues processed: 107 average time/residue: 0.1523 time to fit residues: 29.0428 Evaluate side-chains 109 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 837 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 519 MET Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 274 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 98 optimal weight: 20.0000 chunk 168 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 220 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 184 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 344 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 317 optimal weight: 9.9990 chunk 340 optimal weight: 3.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.047099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.035975 restraints weight = 148522.920| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 4.09 r_work: 0.2609 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 28888 Z= 0.243 Angle : 0.552 11.499 39300 Z= 0.276 Chirality : 0.041 0.156 4496 Planarity : 0.003 0.041 4968 Dihedral : 4.013 18.771 3848 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.53 % Allowed : 8.45 % Favored : 91.01 % 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: 1.40 (0.15), residues: 3548 helix: 1.23 (0.13), residues: 1816 sheet: 0.18 (0.25), residues: 484 loop : 1.07 (0.19), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 808 TYR 0.012 0.001 TYR B 938 PHE 0.013 0.001 PHE A 292 TRP 0.013 0.001 TRP A 80 HIS 0.004 0.001 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00550 (28888) covalent geometry : angle 0.55204 (39300) hydrogen bonds : bond 0.03714 ( 1500) hydrogen bonds : angle 4.25494 ( 4041) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 1.117 Fit side-chains REVERT: A 511 MET cc_start: 0.8815 (ptp) cc_final: 0.8437 (ptp) REVERT: A 713 MET cc_start: 0.9321 (mmt) cc_final: 0.8685 (mmm) REVERT: B 496 MET cc_start: 0.9540 (tpt) cc_final: 0.9220 (tpt) REVERT: B 511 MET cc_start: 0.8729 (ptp) cc_final: 0.8409 (ptp) REVERT: B 713 MET cc_start: 0.9355 (mmt) cc_final: 0.8990 (mmt) REVERT: C 511 MET cc_start: 0.8866 (ptp) cc_final: 0.8485 (ptp) REVERT: C 519 MET cc_start: 0.9544 (OUTLIER) cc_final: 0.9320 (tpt) REVERT: C 713 MET cc_start: 0.9350 (mmt) cc_final: 0.8985 (mmt) REVERT: C 837 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9375 (tt) REVERT: C 915 MET cc_start: 0.9336 (mmm) cc_final: 0.8978 (mmm) REVERT: D 496 MET cc_start: 0.9541 (tpt) cc_final: 0.9215 (tpt) REVERT: D 511 MET cc_start: 0.8749 (ptp) cc_final: 0.8435 (ptp) REVERT: D 519 MET cc_start: 0.9576 (mmm) cc_final: 0.8860 (tmm) REVERT: D 713 MET cc_start: 0.9353 (mmt) cc_final: 0.8986 (mmt) outliers start: 16 outliers final: 11 residues processed: 106 average time/residue: 0.1626 time to fit residues: 30.7721 Evaluate side-chains 105 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 519 MET Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 274 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 6.9990 chunk 201 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 252 optimal weight: 0.4980 chunk 345 optimal weight: 3.9990 chunk 238 optimal weight: 7.9990 chunk 309 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 102 optimal weight: 0.0870 chunk 192 optimal weight: 7.9990 overall best weight: 2.9164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.048053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.036933 restraints weight = 144932.702| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 4.09 r_work: 0.2643 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28888 Z= 0.125 Angle : 0.481 11.252 39300 Z= 0.241 Chirality : 0.040 0.168 4496 Planarity : 0.003 0.043 4968 Dihedral : 3.878 18.359 3848 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.46 % Allowed : 8.52 % Favored : 91.01 % 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: 1.54 (0.15), residues: 3548 helix: 1.34 (0.13), residues: 1812 sheet: 0.27 (0.25), residues: 484 loop : 1.13 (0.19), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 764 TYR 0.011 0.001 TYR C 938 PHE 0.009 0.001 PHE A1010 TRP 0.015 0.001 TRP B 514 HIS 0.002 0.001 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00286 (28888) covalent geometry : angle 0.48140 (39300) hydrogen bonds : bond 0.03435 ( 1500) hydrogen bonds : angle 4.11682 ( 4041) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 1.163 Fit side-chains REVERT: A 511 MET cc_start: 0.8800 (ptp) cc_final: 0.8380 (ptp) REVERT: A 713 MET cc_start: 0.9276 (mmt) cc_final: 0.8656 (mmm) REVERT: B 81 MET cc_start: 0.9232 (mmt) cc_final: 0.8996 (mmt) REVERT: B 496 MET cc_start: 0.9499 (tpt) cc_final: 0.9158 (tpt) REVERT: B 511 MET cc_start: 0.8786 (ptp) cc_final: 0.8563 (ptp) REVERT: B 713 MET cc_start: 0.9298 (mmt) cc_final: 0.8808 (mmt) REVERT: B 852 MET cc_start: 0.9287 (mtp) cc_final: 0.9041 (ttm) REVERT: C 511 MET cc_start: 0.8871 (ptp) cc_final: 0.8454 (ptp) REVERT: C 519 MET cc_start: 0.9548 (OUTLIER) cc_final: 0.9319 (tpt) REVERT: C 713 MET cc_start: 0.9294 (mmt) cc_final: 0.8804 (mmt) REVERT: C 837 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9340 (tt) REVERT: C 915 MET cc_start: 0.9329 (mmm) cc_final: 0.9008 (mmm) REVERT: D 496 MET cc_start: 0.9500 (tpt) cc_final: 0.9176 (tpt) REVERT: D 511 MET cc_start: 0.8791 (ptp) cc_final: 0.8575 (ptp) REVERT: D 519 MET cc_start: 0.9572 (mmm) cc_final: 0.8824 (tmm) REVERT: D 713 MET cc_start: 0.9291 (mmt) cc_final: 0.8801 (mmt) REVERT: D 852 MET cc_start: 0.9278 (mtp) cc_final: 0.9034 (ttm) outliers start: 14 outliers final: 10 residues processed: 104 average time/residue: 0.1644 time to fit residues: 30.3134 Evaluate side-chains 104 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 519 MET Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 209 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 266 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 195 optimal weight: 3.9990 chunk 209 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 218 optimal weight: 9.9990 chunk 199 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.048299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.037210 restraints weight = 145444.067| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 4.09 r_work: 0.2656 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28888 Z= 0.118 Angle : 0.470 10.937 39300 Z= 0.236 Chirality : 0.039 0.186 4496 Planarity : 0.003 0.042 4968 Dihedral : 3.753 18.408 3848 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.43 % Allowed : 8.69 % Favored : 90.88 % 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: 1.63 (0.15), residues: 3548 helix: 1.41 (0.13), residues: 1812 sheet: 0.31 (0.25), residues: 484 loop : 1.18 (0.19), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 432 TYR 0.011 0.001 TYR C 117 PHE 0.008 0.001 PHE C 292 TRP 0.016 0.001 TRP A 80 HIS 0.002 0.001 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00268 (28888) covalent geometry : angle 0.46962 (39300) hydrogen bonds : bond 0.03295 ( 1500) hydrogen bonds : angle 4.06209 ( 4041) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4127.82 seconds wall clock time: 72 minutes 29.16 seconds (4349.16 seconds total)