Starting phenix.real_space_refine on Sun Jul 5 16:32:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rjt_24490/07_2026/7rjt_24490.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rjt_24490/07_2026/7rjt_24490.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rjt_24490/07_2026/7rjt_24490.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rjt_24490/07_2026/7rjt_24490.map" model { file = "/net/cci-nas-00/data/ceres_data/7rjt_24490/07_2026/7rjt_24490.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rjt_24490/07_2026/7rjt_24490.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7rjt_24490/07_2026/7rjt_24490.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rjt_24490/07_2026/7rjt_24490.cif" } resolution = 2.93 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ba 9 18.26 5 K 3 8.98 5 P 4 5.49 5 S 176 5.16 5 C 18736 2.51 5 N 4768 2.21 5 O 5276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28972 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 7188 Classifications: {'peptide': 902} Link IDs: {'PTRANS': 36, 'TRANS': 865} Chain breaks: 4 Chain: "B" Number of atoms: 7188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 7188 Classifications: {'peptide': 902} Link IDs: {'PTRANS': 36, 'TRANS': 865} Chain breaks: 4 Chain: "C" Number of atoms: 7188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 7188 Classifications: {'peptide': 902} Link IDs: {'PTRANS': 36, 'TRANS': 865} Chain breaks: 4 Chain: "D" Number of atoms: 7188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 7188 Classifications: {'peptide': 902} Link IDs: {'PTRANS': 36, 'TRANS': 865} Chain breaks: 4 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 52 Unusual residues: {' K': 3, ' BA': 3, 'PGW': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PGW:plan-1': 3, 'PGW:plan-2': 4, 'PGW:plan-3': 3} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 48 Unusual residues: {' BA': 2, 'PGW': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PGW:plan-1': 3, 'PGW:plan-2': 4, 'PGW:plan-3': 3} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 48 Unusual residues: {' BA': 2, 'PGW': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PGW:plan-1': 3, 'PGW:plan-2': 4, 'PGW:plan-3': 3} Unresolved non-hydrogen planarities: 29 Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 48 Unusual residues: {' BA': 2, 'PGW': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PGW:plan-1': 3, 'PGW:plan-2': 4, 'PGW:plan-3': 3} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 5.44, per 1000 atoms: 0.19 Number of scatterers: 28972 At special positions: 0 Unit cell: (172.764, 172.764, 129.287, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ba 9 55.98 K 3 19.00 S 176 16.00 P 4 15.00 O 5276 8.00 N 4768 7.00 C 18736 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: 2.53 Conformation dependent library (CDL) restraints added in 1.2 seconds 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6808 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 20 sheets defined 52.8% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 16 through 43 removed outlier: 3.978A pdb=" N SER A 22 " --> pdb=" O SER A 18 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER A 23 " --> pdb=" O PHE A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 96 through 123 Processing helix chain 'A' and resid 136 through 159 Processing helix chain 'A' and resid 162 through 167 removed outlier: 3.545A pdb=" N PHE A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TRP A 167 " --> pdb=" O LYS A 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 162 through 167' Processing helix chain 'A' and resid 169 through 189 Proline residue: A 180 - end of helix Processing helix chain 'A' and resid 195 through 204 Processing helix chain 'A' and resid 205 through 214 Processing helix chain 'A' and resid 218 through 249 removed outlier: 4.142A pdb=" N GLY A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 275 Processing helix chain 'A' and resid 286 through 306 removed outlier: 3.551A pdb=" N SER A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.738A pdb=" N ILE A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 353 Processing helix chain 'A' and resid 373 through 383 Processing helix chain 'A' and resid 398 through 403 removed outlier: 3.566A pdb=" N ARG A 402 " --> pdb=" O ASN A 398 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL A 403 " --> pdb=" O ASP A 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 398 through 403' Processing helix chain 'A' and resid 421 through 440 Processing helix chain 'A' and resid 452 through 460 removed outlier: 3.643A pdb=" N ALA A 456 " --> pdb=" O HIS A 453 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 458 " --> pdb=" O LYS A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 469 removed outlier: 3.534A pdb=" N ARG A 468 " --> pdb=" O ASP A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 489 Processing helix chain 'A' and resid 491 through 500 removed outlier: 3.649A pdb=" N LEU A 495 " --> pdb=" O GLY A 491 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE A 500 " --> pdb=" O MET A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 523 removed outlier: 3.595A pdb=" N GLY A 521 " --> pdb=" O ASP A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 536 Processing helix chain 'A' and resid 540 through 550 Processing helix chain 'A' and resid 592 through 601 removed outlier: 3.934A pdb=" N VAL A 596 " --> pdb=" O SER A 592 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS A 597 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE A 600 " --> pdb=" O VAL A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 725 Processing helix chain 'A' and resid 728 through 735 Processing helix chain 'A' and resid 756 through 761 Processing helix chain 'A' and resid 762 through 765 removed outlier: 3.817A pdb=" N ALA A 765 " --> pdb=" O PRO A 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 762 through 765' Processing helix chain 'A' and resid 769 through 773 removed outlier: 3.583A pdb=" N LEU A 773 " --> pdb=" O TYR A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 789 Processing helix chain 'A' and resid 790 through 792 No H-bonds generated for 'chain 'A' and resid 790 through 792' Processing helix chain 'A' and resid 807 through 815 removed outlier: 3.747A pdb=" N LEU A 811 " --> pdb=" O ASN A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 838 removed outlier: 3.951A pdb=" N VAL A 838 " --> pdb=" O PRO A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 852 Processing helix chain 'A' and resid 894 through 901 removed outlier: 3.567A pdb=" N ASN A 897 " --> pdb=" O ASN A 894 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL A 898 " --> pdb=" O ASP A 895 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLN A 899 " --> pdb=" O SER A 896 " (cutoff:3.500A) 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 removed outlier: 3.675A pdb=" N THR A 936 " --> pdb=" O SER A 932 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER A 937 " --> pdb=" O LEU A 933 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A 938 " --> pdb=" O MET A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 953 removed outlier: 3.541A pdb=" N GLY A 953 " --> pdb=" O THR A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 964 Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 997 through 1001 removed outlier: 3.547A pdb=" N PHE A1000 " --> pdb=" O LEU A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1017 Processing helix chain 'B' and resid 16 through 43 removed outlier: 3.978A pdb=" N SER B 22 " --> pdb=" O SER B 18 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER B 23 " --> pdb=" O PHE B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 92 Processing helix chain 'B' and resid 96 through 123 Processing helix chain 'B' and resid 136 through 159 Processing helix chain 'B' and resid 162 through 167 removed outlier: 3.545A pdb=" N PHE B 166 " --> pdb=" O ASP B 162 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TRP B 167 " --> pdb=" O LYS B 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 162 through 167' Processing helix chain 'B' and resid 169 through 189 Proline residue: B 180 - end of helix Processing helix chain 'B' and resid 195 through 204 Processing helix chain 'B' and resid 205 through 214 Processing helix chain 'B' and resid 218 through 249 removed outlier: 4.142A pdb=" N GLY B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 275 Processing helix chain 'B' and resid 286 through 306 removed outlier: 3.551A pdb=" N SER B 306 " --> pdb=" O GLY B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.738A pdb=" N ILE B 311 " --> pdb=" O PHE B 307 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY B 316 " --> pdb=" O ALA B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 353 Processing helix chain 'B' and resid 373 through 383 Processing helix chain 'B' and resid 398 through 403 removed outlier: 3.566A pdb=" N ARG B 402 " --> pdb=" O ASN B 398 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 403 " --> pdb=" O ASP B 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 398 through 403' Processing helix chain 'B' and resid 421 through 440 Processing helix chain 'B' and resid 452 through 460 removed outlier: 3.644A pdb=" N ALA B 456 " --> pdb=" O HIS B 453 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 458 " --> pdb=" O LYS B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 469 removed outlier: 3.534A pdb=" N ARG B 468 " --> pdb=" O ASP B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 Processing helix chain 'B' and resid 491 through 500 removed outlier: 3.649A pdb=" N LEU B 495 " --> pdb=" O GLY B 491 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE B 500 " --> pdb=" O MET B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 523 removed outlier: 3.595A pdb=" N GLY B 521 " --> pdb=" O ASP B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 536 Processing helix chain 'B' and resid 540 through 550 Processing helix chain 'B' and resid 592 through 601 removed outlier: 3.934A pdb=" N VAL B 596 " --> pdb=" O SER B 592 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS B 597 " --> pdb=" O ALA B 593 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG B 598 " --> pdb=" O GLU B 594 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA B 599 " --> pdb=" O GLU B 595 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE B 600 " --> pdb=" O VAL B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 725 Processing helix chain 'B' and resid 728 through 735 Processing helix chain 'B' and resid 756 through 761 Processing helix chain 'B' and resid 762 through 765 removed outlier: 3.817A pdb=" N ALA B 765 " --> pdb=" O PRO B 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 762 through 765' Processing helix chain 'B' and resid 769 through 773 removed outlier: 3.583A pdb=" N LEU B 773 " --> pdb=" O TYR B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 789 Processing helix chain 'B' and resid 790 through 792 No H-bonds generated for 'chain 'B' and resid 790 through 792' Processing helix chain 'B' and resid 807 through 815 removed outlier: 3.747A pdb=" N LEU B 811 " --> pdb=" O ASN B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 838 removed outlier: 3.951A pdb=" N VAL B 838 " --> pdb=" O PRO B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 852 Processing helix chain 'B' and resid 894 through 901 removed outlier: 3.567A pdb=" N ASN B 897 " --> pdb=" O ASN B 894 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL B 898 " --> pdb=" O ASP B 895 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN B 899 " --> pdb=" O SER B 896 " (cutoff:3.500A) 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 removed outlier: 3.675A pdb=" N THR B 936 " --> pdb=" O SER B 932 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B 937 " --> pdb=" O LEU B 933 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR B 938 " --> pdb=" O MET B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 953 removed outlier: 3.541A pdb=" N GLY B 953 " --> pdb=" O THR B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 964 Processing helix chain 'B' and resid 977 through 982 Processing helix chain 'B' and resid 997 through 1001 removed outlier: 3.547A pdb=" N PHE B1000 " --> pdb=" O LEU B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1017 Processing helix chain 'C' and resid 16 through 43 removed outlier: 3.978A pdb=" N SER C 22 " --> pdb=" O SER C 18 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER C 23 " --> pdb=" O PHE C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 92 Processing helix chain 'C' and resid 96 through 123 Processing helix chain 'C' and resid 136 through 159 Processing helix chain 'C' and resid 162 through 167 removed outlier: 3.545A pdb=" N PHE C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TRP C 167 " --> pdb=" O LYS C 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 162 through 167' Processing helix chain 'C' and resid 169 through 189 Proline residue: C 180 - end of helix Processing helix chain 'C' and resid 195 through 204 Processing helix chain 'C' and resid 205 through 214 Processing helix chain 'C' and resid 218 through 249 removed outlier: 4.142A pdb=" N GLY C 249 " --> pdb=" O LEU C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 275 Processing helix chain 'C' and resid 286 through 306 removed outlier: 3.551A pdb=" N SER C 306 " --> pdb=" O GLY C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.738A pdb=" N ILE C 311 " --> pdb=" O PHE C 307 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY C 316 " --> pdb=" O ALA C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 353 Processing helix chain 'C' and resid 373 through 383 Processing helix chain 'C' and resid 398 through 403 removed outlier: 3.567A pdb=" N ARG C 402 " --> pdb=" O ASN C 398 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL C 403 " --> pdb=" O ASP C 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 398 through 403' Processing helix chain 'C' and resid 421 through 440 Processing helix chain 'C' and resid 452 through 460 removed outlier: 3.644A pdb=" N ALA C 456 " --> pdb=" O HIS C 453 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU C 458 " --> pdb=" O LYS C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 469 removed outlier: 3.534A pdb=" N ARG C 468 " --> pdb=" O ASP C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 489 Processing helix chain 'C' and resid 491 through 500 removed outlier: 3.649A pdb=" N LEU C 495 " --> pdb=" O GLY C 491 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE C 500 " --> pdb=" O MET C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 523 removed outlier: 3.595A pdb=" N GLY C 521 " --> pdb=" O ASP C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 536 Processing helix chain 'C' and resid 540 through 550 Processing helix chain 'C' and resid 592 through 601 removed outlier: 3.934A pdb=" N VAL C 596 " --> pdb=" O SER C 592 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS C 597 " --> pdb=" O ALA C 593 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG C 598 " --> pdb=" O GLU C 594 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA C 599 " --> pdb=" O GLU C 595 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE C 600 " --> pdb=" O VAL C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 725 Processing helix chain 'C' and resid 728 through 735 Processing helix chain 'C' and resid 756 through 761 Processing helix chain 'C' and resid 762 through 765 removed outlier: 3.817A pdb=" N ALA C 765 " --> pdb=" O PRO C 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 762 through 765' Processing helix chain 'C' and resid 769 through 773 removed outlier: 3.583A pdb=" N LEU C 773 " --> pdb=" O TYR C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 789 Processing helix chain 'C' and resid 790 through 792 No H-bonds generated for 'chain 'C' and resid 790 through 792' Processing helix chain 'C' and resid 807 through 815 removed outlier: 3.747A pdb=" N LEU C 811 " --> pdb=" O ASN C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 838 removed outlier: 3.951A pdb=" N VAL C 838 " --> pdb=" O PRO C 835 " (cutoff:3.500A) Processing helix chain 'C' and resid 839 through 852 Processing helix chain 'C' and resid 894 through 901 removed outlier: 3.567A pdb=" N ASN C 897 " --> pdb=" O ASN C 894 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL C 898 " --> pdb=" O ASP C 895 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN C 899 " --> pdb=" O SER C 896 " (cutoff:3.500A) 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 removed outlier: 3.676A pdb=" N THR C 936 " --> pdb=" O SER C 932 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER C 937 " --> pdb=" O LEU C 933 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR C 938 " --> pdb=" O MET C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 953 removed outlier: 3.542A pdb=" N GLY C 953 " --> pdb=" O THR C 949 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 964 Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 997 through 1001 removed outlier: 3.547A pdb=" N PHE C1000 " --> pdb=" O LEU C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1017 Processing helix chain 'D' and resid 16 through 43 removed outlier: 3.978A pdb=" N SER D 22 " --> pdb=" O SER D 18 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER D 23 " --> pdb=" O PHE D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 96 through 123 Processing helix chain 'D' and resid 136 through 159 Processing helix chain 'D' and resid 162 through 167 removed outlier: 3.545A pdb=" N PHE D 166 " --> pdb=" O ASP D 162 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TRP D 167 " --> pdb=" O LYS D 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 162 through 167' Processing helix chain 'D' and resid 169 through 189 Proline residue: D 180 - end of helix Processing helix chain 'D' and resid 195 through 204 Processing helix chain 'D' and resid 205 through 214 Processing helix chain 'D' and resid 218 through 249 removed outlier: 4.142A pdb=" N GLY D 249 " --> pdb=" O LEU D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 275 Processing helix chain 'D' and resid 286 through 306 removed outlier: 3.551A pdb=" N SER D 306 " --> pdb=" O GLY D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 316 removed outlier: 3.738A pdb=" N ILE D 311 " --> pdb=" O PHE D 307 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY D 316 " --> pdb=" O ALA D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 353 Processing helix chain 'D' and resid 373 through 383 Processing helix chain 'D' and resid 398 through 403 removed outlier: 3.567A pdb=" N ARG D 402 " --> pdb=" O ASN D 398 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL D 403 " --> pdb=" O ASP D 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 398 through 403' Processing helix chain 'D' and resid 421 through 440 Processing helix chain 'D' and resid 452 through 460 removed outlier: 3.643A pdb=" N ALA D 456 " --> pdb=" O HIS D 453 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU D 458 " --> pdb=" O LYS D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 469 removed outlier: 3.534A pdb=" N ARG D 468 " --> pdb=" O ASP D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 489 Processing helix chain 'D' and resid 491 through 500 removed outlier: 3.649A pdb=" N LEU D 495 " --> pdb=" O GLY D 491 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE D 500 " --> pdb=" O MET D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 523 removed outlier: 3.595A pdb=" N GLY D 521 " --> pdb=" O ASP D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 536 Processing helix chain 'D' and resid 540 through 550 Processing helix chain 'D' and resid 592 through 601 removed outlier: 3.934A pdb=" N VAL D 596 " --> pdb=" O SER D 592 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS D 597 " --> pdb=" O ALA D 593 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG D 598 " --> pdb=" O GLU D 594 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ALA D 599 " --> pdb=" O GLU D 595 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE D 600 " --> pdb=" O VAL D 596 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 725 Processing helix chain 'D' and resid 728 through 735 Processing helix chain 'D' and resid 756 through 761 Processing helix chain 'D' and resid 762 through 765 removed outlier: 3.817A pdb=" N ALA D 765 " --> pdb=" O PRO D 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 762 through 765' Processing helix chain 'D' and resid 769 through 773 removed outlier: 3.583A pdb=" N LEU D 773 " --> pdb=" O TYR D 770 " (cutoff:3.500A) Processing helix chain 'D' and resid 782 through 789 Processing helix chain 'D' and resid 790 through 792 No H-bonds generated for 'chain 'D' and resid 790 through 792' Processing helix chain 'D' and resid 807 through 815 removed outlier: 3.747A pdb=" N LEU D 811 " --> pdb=" O ASN D 807 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 838 removed outlier: 3.951A pdb=" N VAL D 838 " --> pdb=" O PRO D 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 839 through 852 Processing helix chain 'D' and resid 894 through 901 removed outlier: 3.567A pdb=" N ASN D 897 " --> pdb=" O ASN D 894 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL D 898 " --> pdb=" O ASP D 895 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLN D 899 " --> pdb=" O SER D 896 " (cutoff:3.500A) 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 removed outlier: 3.676A pdb=" N THR D 936 " --> pdb=" O SER D 932 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER D 937 " --> pdb=" O LEU D 933 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR D 938 " --> pdb=" O MET D 934 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 953 removed outlier: 3.542A pdb=" N GLY D 953 " --> pdb=" O THR D 949 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 964 Processing helix chain 'D' and resid 977 through 982 Processing helix chain 'D' and resid 997 through 1001 removed outlier: 3.547A pdb=" N PHE D1000 " --> pdb=" O LEU D 997 " (cutoff:3.500A) Processing helix chain 'D' and resid 1005 through 1017 Processing sheet with id=AA1, first strand: chain 'A' and resid 387 through 391 removed outlier: 7.006A pdb=" N ARG A 332 " --> pdb=" O GLU A 363 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VAL A 365 " --> pdb=" O ARG A 332 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A 334 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU A 367 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL A 336 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N HIS A 333 " --> pdb=" O ALA A 410 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N LEU A 412 " --> pdb=" O HIS A 333 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL A 335 " --> pdb=" O LEU A 412 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 525 through 530 removed outlier: 5.088A pdb=" N GLN A 585 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA A 557 " --> pdb=" O PHE A 587 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE A 589 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU A 555 " --> pdb=" O ILE A 589 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 539 removed outlier: 3.918A pdb=" N LEU A 538 " --> pdb=" O ILE A 580 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 798 through 802 removed outlier: 6.457A pdb=" N THR A 776 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU A 801 " --> pdb=" O THR A 776 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE A 778 " --> pdb=" O LEU A 801 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N SER A 826 " --> pdb=" O GLU A 891 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 986 through 991 removed outlier: 3.943A pdb=" N GLY A1023 " --> pdb=" O TYR A1060 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU A1062 " --> pdb=" O CYS A1021 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N CYS A1021 " --> pdb=" O LEU A1062 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 387 through 391 removed outlier: 7.006A pdb=" N ARG B 332 " --> pdb=" O GLU B 363 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VAL B 365 " --> pdb=" O ARG B 332 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL B 334 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU B 367 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL B 336 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N HIS B 333 " --> pdb=" O ALA B 410 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N LEU B 412 " --> pdb=" O HIS B 333 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL B 335 " --> pdb=" O LEU B 412 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 525 through 530 removed outlier: 5.088A pdb=" N GLN B 585 " --> pdb=" O GLU B 559 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA B 557 " --> pdb=" O PHE B 587 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE B 589 " --> pdb=" O LEU B 555 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU B 555 " --> pdb=" O ILE B 589 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 538 through 539 removed outlier: 3.918A pdb=" N LEU B 538 " --> pdb=" O ILE B 580 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 798 through 802 removed outlier: 6.457A pdb=" N THR B 776 " --> pdb=" O SER B 799 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU B 801 " --> pdb=" O THR B 776 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE B 778 " --> pdb=" O LEU B 801 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N SER B 826 " --> pdb=" O GLU B 891 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 986 through 991 removed outlier: 3.943A pdb=" N GLY B1023 " --> pdb=" O TYR B1060 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU B1062 " --> pdb=" O CYS B1021 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N CYS B1021 " --> pdb=" O LEU B1062 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 387 through 391 removed outlier: 7.006A pdb=" N ARG C 332 " --> pdb=" O GLU C 363 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VAL C 365 " --> pdb=" O ARG C 332 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL C 334 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU C 367 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL C 336 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N HIS C 333 " --> pdb=" O ALA C 410 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N LEU C 412 " --> pdb=" O HIS C 333 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL C 335 " --> pdb=" O LEU C 412 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 525 through 530 removed outlier: 5.088A pdb=" N GLN C 585 " --> pdb=" O GLU C 559 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA C 557 " --> pdb=" O PHE C 587 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE C 589 " --> pdb=" O LEU C 555 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU C 555 " --> pdb=" O ILE C 589 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 538 through 539 removed outlier: 3.918A pdb=" N LEU C 538 " --> pdb=" O ILE C 580 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 798 through 802 removed outlier: 6.456A pdb=" N THR C 776 " --> pdb=" O SER C 799 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LEU C 801 " --> pdb=" O THR C 776 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE C 778 " --> pdb=" O LEU C 801 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N SER C 826 " --> pdb=" O GLU C 891 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 986 through 991 removed outlier: 3.943A pdb=" N GLY C1023 " --> pdb=" O TYR C1060 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU C1062 " --> pdb=" O CYS C1021 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N CYS C1021 " --> pdb=" O LEU C1062 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 387 through 391 removed outlier: 7.006A pdb=" N ARG D 332 " --> pdb=" O GLU D 363 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VAL D 365 " --> pdb=" O ARG D 332 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL D 334 " --> pdb=" O VAL D 365 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU D 367 " --> pdb=" O VAL D 334 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL D 336 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N HIS D 333 " --> pdb=" O ALA D 410 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N LEU D 412 " --> pdb=" O HIS D 333 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL D 335 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 525 through 530 removed outlier: 5.088A pdb=" N GLN D 585 " --> pdb=" O GLU D 559 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA D 557 " --> pdb=" O PHE D 587 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE D 589 " --> pdb=" O LEU D 555 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU D 555 " --> pdb=" O ILE D 589 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 538 through 539 removed outlier: 3.918A pdb=" N LEU D 538 " --> pdb=" O ILE D 580 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 798 through 802 removed outlier: 6.456A pdb=" N THR D 776 " --> pdb=" O SER D 799 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LEU D 801 " --> pdb=" O THR D 776 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE D 778 " --> pdb=" O LEU D 801 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N SER D 826 " --> pdb=" O GLU D 891 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 986 through 991 removed outlier: 3.943A pdb=" N GLY D1023 " --> pdb=" O TYR D1060 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU D1062 " --> pdb=" O CYS D1021 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N CYS D1021 " --> pdb=" O LEU D1062 " (cutoff:3.500A) 1312 hydrogen bonds defined for protein. 3576 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: 5.31 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5773 1.33 - 1.45: 7118 1.45 - 1.57: 16437 1.57 - 1.69: 4 1.69 - 1.81: 268 Bond restraints: 29600 Sorted by residual: bond pdb=" C10 PGW B1103 " pdb=" C9 PGW B1103 " ideal model delta sigma weight residual 1.333 1.564 -0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C10 PGW C1103 " pdb=" C9 PGW C1103 " ideal model delta sigma weight residual 1.333 1.564 -0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C10 PGW A1103 " pdb=" C9 PGW A1103 " ideal model delta sigma weight residual 1.333 1.564 -0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C10 PGW D1103 " pdb=" C9 PGW D1103 " ideal model delta sigma weight residual 1.333 1.564 -0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" O14 PGW D1106 " pdb=" P PGW D1106 " ideal model delta sigma weight residual 1.512 1.731 -0.219 2.00e-02 2.50e+03 1.20e+02 ... (remaining 29595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 39884 3.16 - 6.32: 204 6.32 - 9.48: 8 9.48 - 12.65: 8 12.65 - 15.81: 8 Bond angle restraints: 40112 Sorted by residual: angle pdb=" O12 PGW C1106 " pdb=" P PGW C1106 " pdb=" O13 PGW C1106 " ideal model delta sigma weight residual 111.13 126.94 -15.81 3.00e+00 1.11e-01 2.78e+01 angle pdb=" O12 PGW B1106 " pdb=" P PGW B1106 " pdb=" O13 PGW B1106 " ideal model delta sigma weight residual 111.13 126.94 -15.81 3.00e+00 1.11e-01 2.78e+01 angle pdb=" O12 PGW D1106 " pdb=" P PGW D1106 " pdb=" O13 PGW D1106 " ideal model delta sigma weight residual 111.13 126.88 -15.75 3.00e+00 1.11e-01 2.76e+01 angle pdb=" O12 PGW A1106 " pdb=" P PGW A1106 " pdb=" O13 PGW A1106 " ideal model delta sigma weight residual 111.13 126.88 -15.75 3.00e+00 1.11e-01 2.76e+01 angle pdb=" O13 PGW B1106 " pdb=" P PGW B1106 " pdb=" O14 PGW B1106 " ideal model delta sigma weight residual 119.81 104.10 15.71 3.00e+00 1.11e-01 2.74e+01 ... (remaining 40107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 15858 17.48 - 34.96: 1306 34.96 - 52.44: 256 52.44 - 69.92: 96 69.92 - 87.40: 16 Dihedral angle restraints: 17532 sinusoidal: 7000 harmonic: 10532 Sorted by residual: dihedral pdb=" CA TYR D1025 " pdb=" C TYR D1025 " pdb=" N ARG D1026 " pdb=" CA ARG D1026 " ideal model delta harmonic sigma weight residual -180.00 -156.88 -23.12 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA TYR A1025 " pdb=" C TYR A1025 " pdb=" N ARG A1026 " pdb=" CA ARG A1026 " ideal model delta harmonic sigma weight residual -180.00 -156.88 -23.12 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA TYR B1025 " pdb=" C TYR B1025 " pdb=" N ARG B1026 " pdb=" CA ARG B1026 " ideal model delta harmonic sigma weight residual 180.00 -156.90 -23.10 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 17529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2994 0.035 - 0.069: 1124 0.069 - 0.104: 294 0.104 - 0.138: 80 0.138 - 0.173: 8 Chirality restraints: 4500 Sorted by residual: chirality pdb=" CB ILE D 92 " pdb=" CA ILE D 92 " pdb=" CG1 ILE D 92 " pdb=" CG2 ILE D 92 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.45e-01 chirality pdb=" CB ILE C 92 " pdb=" CA ILE C 92 " pdb=" CG1 ILE C 92 " pdb=" CG2 ILE C 92 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.45e-01 chirality pdb=" CB ILE B 92 " pdb=" CA ILE B 92 " pdb=" CG1 ILE B 92 " pdb=" CG2 ILE B 92 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.37e-01 ... (remaining 4497 not shown) Planarity restraints: 5092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW C1103 " -0.024 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C10 PGW C1103 " 0.045 2.00e-02 2.50e+03 pdb=" C8 PGW C1103 " 0.023 2.00e-02 2.50e+03 pdb=" C9 PGW C1103 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW B1103 " 0.023 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C10 PGW B1103 " -0.044 2.00e-02 2.50e+03 pdb=" C8 PGW B1103 " -0.023 2.00e-02 2.50e+03 pdb=" C9 PGW B1103 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW D1103 " -0.023 2.00e-02 2.50e+03 3.51e-02 1.24e+01 pdb=" C10 PGW D1103 " 0.044 2.00e-02 2.50e+03 pdb=" C8 PGW D1103 " 0.023 2.00e-02 2.50e+03 pdb=" C9 PGW D1103 " -0.044 2.00e-02 2.50e+03 ... (remaining 5089 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.83: 9068 2.83 - 3.41: 30426 3.41 - 3.98: 51716 3.98 - 4.56: 74692 4.56 - 5.14: 109747 Nonbonded interactions: 275649 Sorted by model distance: nonbonded pdb=" OH TYR D 321 " pdb=" OE2 GLU D 377 " model vdw 2.251 3.040 nonbonded pdb=" OH TYR A 321 " pdb=" OE2 GLU A 377 " model vdw 2.251 3.040 nonbonded pdb=" OH TYR C 321 " pdb=" OE2 GLU C 377 " model vdw 2.252 3.040 nonbonded pdb=" OH TYR B 321 " pdb=" OE2 GLU B 377 " model vdw 2.252 3.040 nonbonded pdb=" O SER A 463 " pdb=" NH2 ARG A 468 " model vdw 2.298 3.120 ... (remaining 275644 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 11 through 1106) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.980 Find NCS groups from input model: 0.570 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: 0.010 Load rotamer database and sin/cos tables:5.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 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 : 0.005 0.231 29600 Z= 0.262 Angle : 0.591 15.807 40112 Z= 0.273 Chirality : 0.040 0.173 4500 Planarity : 0.003 0.035 5092 Dihedral : 14.116 87.397 10724 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.15), residues: 3568 helix: 1.13 (0.14), residues: 1616 sheet: -0.28 (0.28), residues: 404 loop : -0.05 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1041 TYR 0.030 0.001 TYR C1025 PHE 0.013 0.001 PHE D 107 TRP 0.008 0.001 TRP C 514 HIS 0.010 0.001 HIS D 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.26 (29600) covalent geometry : angle 0.59063 / 0.27 (40112) hydrogen bonds : bond 0.14404 / 9.35 ( 1312) hydrogen bonds : angle 5.07860 / 3.65 ( 3576) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.851 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.6398 time to fit residues: 123.1226 Evaluate side-chains 128 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 ASN A 429 ASN A 438 ASN A 897 ASN B 398 ASN B 429 ASN B 438 ASN B 897 ASN C 398 ASN C 429 ASN C 897 ASN D 398 ASN D 429 ASN D 897 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.188770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.109560 restraints weight = 36872.325| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.62 r_work: 0.3199 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 29600 Z= 0.205 Angle : 0.557 7.198 40112 Z= 0.280 Chirality : 0.044 0.180 4500 Planarity : 0.004 0.037 5092 Dihedral : 8.214 83.453 4016 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.89 % Allowed : 5.37 % Favored : 93.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.15), residues: 3568 helix: 1.06 (0.13), residues: 1628 sheet: -0.49 (0.27), residues: 404 loop : 0.06 (0.17), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 982 TYR 0.034 0.002 TYR A1025 PHE 0.012 0.001 PHE B 500 TRP 0.009 0.001 TRP C 514 HIS 0.007 0.001 HIS B 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.20 (29600) covalent geometry : angle 0.55725 / 0.28 (40112) hydrogen bonds : bond 0.04362 / 2.83 ( 1312) hydrogen bonds : angle 4.36646 / 3.13 ( 3576) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.964 Fit side-chains REVERT: A 526 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7784 (ttp) REVERT: A 905 ASP cc_start: 0.7513 (p0) cc_final: 0.7296 (p0) REVERT: B 526 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7790 (ttp) REVERT: B 905 ASP cc_start: 0.7512 (p0) cc_final: 0.7295 (p0) REVERT: C 388 GLU cc_start: 0.7876 (mp0) cc_final: 0.7451 (mp0) REVERT: C 526 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7779 (ttp) REVERT: C 905 ASP cc_start: 0.7515 (p0) cc_final: 0.7301 (p0) REVERT: D 388 GLU cc_start: 0.7885 (mp0) cc_final: 0.7461 (mp0) REVERT: D 526 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7777 (ttp) REVERT: D 905 ASP cc_start: 0.7512 (p0) cc_final: 0.7302 (p0) outliers start: 28 outliers final: 4 residues processed: 166 average time/residue: 0.7351 time to fit residues: 140.5690 Evaluate side-chains 146 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 PHE Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 526 MET Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 526 MET Chi-restraints excluded: chain D residue 300 PHE Chi-restraints excluded: chain D residue 526 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 240 optimal weight: 0.8980 chunk 11 optimal weight: 50.0000 chunk 320 optimal weight: 8.9990 chunk 218 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 355 optimal weight: 0.9980 chunk 145 optimal weight: 40.0000 chunk 167 optimal weight: 0.8980 chunk 348 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 328 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.191501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.113106 restraints weight = 37042.327| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.62 r_work: 0.3247 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 29600 Z= 0.100 Angle : 0.468 7.902 40112 Z= 0.237 Chirality : 0.040 0.153 4500 Planarity : 0.003 0.037 5092 Dihedral : 7.447 84.896 4016 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.38 % Allowed : 8.04 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.15), residues: 3568 helix: 1.07 (0.13), residues: 1708 sheet: -0.30 (0.27), residues: 404 loop : -0.02 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 982 TYR 0.017 0.001 TYR D1025 PHE 0.010 0.001 PHE D 107 TRP 0.008 0.001 TRP C 514 HIS 0.002 0.001 HIS C 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (29600) covalent geometry : angle 0.46788 / 0.24 (40112) hydrogen bonds : bond 0.03154 / 2.05 ( 1312) hydrogen bonds : angle 4.10081 / 2.93 ( 3576) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.967 Fit side-chains outliers start: 12 outliers final: 0 residues processed: 130 average time/residue: 0.5800 time to fit residues: 89.4454 Evaluate side-chains 130 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 184 optimal weight: 9.9990 chunk 148 optimal weight: 0.4980 chunk 105 optimal weight: 0.4980 chunk 107 optimal weight: 5.9990 chunk 306 optimal weight: 3.9990 chunk 284 optimal weight: 7.9990 chunk 180 optimal weight: 120.0000 chunk 193 optimal weight: 30.0000 chunk 0 optimal weight: 100.0000 chunk 69 optimal weight: 2.9990 chunk 261 optimal weight: 9.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 453 HIS C 438 ASN D 438 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.188549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.109493 restraints weight = 36959.329| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.58 r_work: 0.3190 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 29600 Z= 0.204 Angle : 0.547 7.044 40112 Z= 0.273 Chirality : 0.043 0.136 4500 Planarity : 0.004 0.037 5092 Dihedral : 7.138 87.224 4016 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.14 % Allowed : 9.78 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.15), residues: 3568 helix: 1.21 (0.13), residues: 1636 sheet: -0.44 (0.27), residues: 404 loop : 0.03 (0.17), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 984 TYR 0.021 0.001 TYR C1025 PHE 0.013 0.001 PHE C 500 TRP 0.009 0.001 TRP C 514 HIS 0.007 0.001 HIS B 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.20 (29600) covalent geometry : angle 0.54740 / 0.27 (40112) hydrogen bonds : bond 0.04051 / 2.62 ( 1312) hydrogen bonds : angle 4.19155 / 3.00 ( 3576) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 1.051 Fit side-chains REVERT: A 388 GLU cc_start: 0.7852 (mp0) cc_final: 0.7367 (mp0) REVERT: A 438 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.8182 (t0) REVERT: A 494 THR cc_start: 0.8995 (OUTLIER) cc_final: 0.8709 (p) REVERT: A 905 ASP cc_start: 0.7848 (p0) cc_final: 0.7542 (p0) REVERT: B 388 GLU cc_start: 0.7858 (mp0) cc_final: 0.7370 (mp0) REVERT: B 438 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.8182 (t0) REVERT: B 494 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8710 (p) REVERT: B 905 ASP cc_start: 0.7834 (p0) cc_final: 0.7533 (p0) REVERT: C 388 GLU cc_start: 0.7845 (mp0) cc_final: 0.7355 (mp0) REVERT: C 438 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.8084 (OUTLIER) REVERT: C 494 THR cc_start: 0.8995 (OUTLIER) cc_final: 0.8707 (p) REVERT: C 905 ASP cc_start: 0.7831 (p0) cc_final: 0.7528 (p0) REVERT: D 388 GLU cc_start: 0.7853 (mp0) cc_final: 0.7365 (mp0) REVERT: D 438 ASN cc_start: 0.8427 (OUTLIER) cc_final: 0.8081 (OUTLIER) REVERT: D 494 THR cc_start: 0.8999 (OUTLIER) cc_final: 0.8710 (p) REVERT: D 905 ASP cc_start: 0.7842 (p0) cc_final: 0.7543 (p0) outliers start: 36 outliers final: 4 residues processed: 164 average time/residue: 0.6110 time to fit residues: 119.1297 Evaluate side-chains 142 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 969 MET Chi-restraints excluded: chain C residue 438 ASN Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 969 MET Chi-restraints excluded: chain D residue 438 ASN Chi-restraints excluded: chain D residue 494 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 354 optimal weight: 6.9990 chunk 269 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 136 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 198 optimal weight: 30.0000 chunk 227 optimal weight: 9.9990 chunk 256 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 195 optimal weight: 0.4980 chunk 352 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.192839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.110069 restraints weight = 37777.226| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.85 r_work: 0.3178 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29600 Z= 0.139 Angle : 0.491 7.704 40112 Z= 0.248 Chirality : 0.040 0.133 4500 Planarity : 0.003 0.036 5092 Dihedral : 6.762 88.784 4016 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.95 % Allowed : 10.99 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.15), residues: 3568 helix: 1.07 (0.13), residues: 1708 sheet: -0.39 (0.27), residues: 400 loop : -0.11 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 503 TYR 0.013 0.001 TYR B1025 PHE 0.008 0.001 PHE A 500 TRP 0.010 0.001 TRP C 514 HIS 0.003 0.001 HIS A 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (29600) covalent geometry : angle 0.49125 / 0.25 (40112) hydrogen bonds : bond 0.03427 / 2.23 ( 1312) hydrogen bonds : angle 4.08648 / 2.92 ( 3576) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 1.034 Fit side-chains REVERT: A 388 GLU cc_start: 0.7679 (mp0) cc_final: 0.7193 (mp0) REVERT: A 438 ASN cc_start: 0.8001 (OUTLIER) cc_final: 0.7606 (t0) REVERT: B 388 GLU cc_start: 0.7681 (mp0) cc_final: 0.7192 (mp0) REVERT: B 438 ASN cc_start: 0.8003 (OUTLIER) cc_final: 0.7613 (t0) REVERT: C 388 GLU cc_start: 0.7668 (mp0) cc_final: 0.7174 (mp0) REVERT: D 388 GLU cc_start: 0.7672 (mp0) cc_final: 0.7178 (mp0) outliers start: 30 outliers final: 4 residues processed: 150 average time/residue: 0.6580 time to fit residues: 116.2346 Evaluate side-chains 138 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 522 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 185 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 159 optimal weight: 0.7980 chunk 320 optimal weight: 8.9990 chunk 246 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 207 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 453 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.193059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.110509 restraints weight = 37840.651| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.85 r_work: 0.3197 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 29600 Z= 0.118 Angle : 0.480 7.411 40112 Z= 0.242 Chirality : 0.040 0.133 4500 Planarity : 0.003 0.036 5092 Dihedral : 6.329 89.405 4016 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.70 % Allowed : 12.07 % Favored : 87.23 % 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 are not related in a simple way. whole: 0.55 (0.15), residues: 3568 helix: 1.06 (0.13), residues: 1732 sheet: -0.30 (0.27), residues: 400 loop : -0.17 (0.17), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 503 TYR 0.011 0.001 TYR A1025 PHE 0.030 0.001 PHE D 300 TRP 0.010 0.001 TRP B 514 HIS 0.003 0.001 HIS D 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (29600) covalent geometry : angle 0.47997 / 0.24 (40112) hydrogen bonds : bond 0.03212 / 2.09 ( 1312) hydrogen bonds : angle 3.99664 / 2.85 ( 3576) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 1.047 Fit side-chains REVERT: A 388 GLU cc_start: 0.7634 (mp0) cc_final: 0.7161 (mp0) REVERT: A 438 ASN cc_start: 0.7933 (OUTLIER) cc_final: 0.7566 (t0) REVERT: A 494 THR cc_start: 0.8871 (OUTLIER) cc_final: 0.8595 (p) REVERT: A 905 ASP cc_start: 0.7821 (p0) cc_final: 0.7601 (p0) REVERT: B 388 GLU cc_start: 0.7632 (mp0) cc_final: 0.7157 (mp0) REVERT: B 438 ASN cc_start: 0.7933 (OUTLIER) cc_final: 0.7570 (t0) REVERT: B 494 THR cc_start: 0.8871 (OUTLIER) cc_final: 0.8596 (p) REVERT: B 905 ASP cc_start: 0.7765 (p0) cc_final: 0.7495 (p0) REVERT: C 388 GLU cc_start: 0.7620 (mp0) cc_final: 0.7143 (mp0) REVERT: C 494 THR cc_start: 0.8876 (OUTLIER) cc_final: 0.8598 (p) REVERT: C 905 ASP cc_start: 0.7773 (p0) cc_final: 0.7499 (p0) REVERT: D 388 GLU cc_start: 0.7627 (mp0) cc_final: 0.7150 (mp0) REVERT: D 494 THR cc_start: 0.8882 (OUTLIER) cc_final: 0.8602 (p) REVERT: D 905 ASP cc_start: 0.7804 (p0) cc_final: 0.7600 (p0) outliers start: 22 outliers final: 8 residues processed: 150 average time/residue: 0.5425 time to fit residues: 97.5373 Evaluate side-chains 146 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 522 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 279 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 354 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 113 optimal weight: 7.9990 chunk 288 optimal weight: 30.0000 chunk 184 optimal weight: 50.0000 chunk 73 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 chunk 276 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 453 HIS B1046 ASN C 438 ASN C1046 ASN D 438 ASN D 453 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.191460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.108516 restraints weight = 37885.682| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.84 r_work: 0.3168 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 29600 Z= 0.187 Angle : 0.521 6.991 40112 Z= 0.262 Chirality : 0.042 0.135 4500 Planarity : 0.004 0.036 5092 Dihedral : 5.987 86.350 4016 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.14 % Allowed : 12.01 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.15), residues: 3568 helix: 1.27 (0.13), residues: 1656 sheet: -0.37 (0.27), residues: 400 loop : -0.09 (0.17), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 503 TYR 0.013 0.001 TYR C1025 PHE 0.027 0.001 PHE C 300 TRP 0.009 0.001 TRP D 514 HIS 0.005 0.001 HIS B 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.19 (29600) covalent geometry : angle 0.52146 / 0.26 (40112) hydrogen bonds : bond 0.03757 / 2.44 ( 1312) hydrogen bonds : angle 4.06654 / 2.91 ( 3576) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 1.111 Fit side-chains REVERT: A 388 GLU cc_start: 0.7766 (mp0) cc_final: 0.7238 (mp0) REVERT: A 438 ASN cc_start: 0.8218 (OUTLIER) cc_final: 0.7826 (t0) REVERT: A 494 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8622 (p) REVERT: A 706 ARG cc_start: 0.7690 (mmt180) cc_final: 0.7239 (mmt180) REVERT: B 388 GLU cc_start: 0.7761 (mp0) cc_final: 0.7227 (mp0) REVERT: B 438 ASN cc_start: 0.8211 (OUTLIER) cc_final: 0.7826 (t0) REVERT: B 494 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8624 (p) REVERT: B 706 ARG cc_start: 0.7690 (mmt180) cc_final: 0.7237 (mmt180) REVERT: C 388 GLU cc_start: 0.7759 (mp0) cc_final: 0.7244 (mp0) REVERT: C 438 ASN cc_start: 0.8311 (OUTLIER) cc_final: 0.7877 (OUTLIER) REVERT: C 494 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8623 (p) REVERT: D 388 GLU cc_start: 0.7756 (mp0) cc_final: 0.7239 (mp0) REVERT: D 438 ASN cc_start: 0.8301 (OUTLIER) cc_final: 0.7858 (OUTLIER) REVERT: D 494 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8626 (p) REVERT: D 706 ARG cc_start: 0.7695 (mmt180) cc_final: 0.7244 (mmt180) outliers start: 36 outliers final: 10 residues processed: 161 average time/residue: 0.6496 time to fit residues: 123.2401 Evaluate side-chains 147 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain C residue 438 ASN Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 927 VAL Chi-restraints excluded: chain D residue 438 ASN Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 927 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 104 optimal weight: 4.9990 chunk 208 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 199 optimal weight: 50.0000 chunk 258 optimal weight: 0.9980 chunk 156 optimal weight: 0.7980 chunk 165 optimal weight: 0.9980 chunk 265 optimal weight: 0.6980 chunk 327 optimal weight: 0.9980 chunk 66 optimal weight: 0.0970 chunk 189 optimal weight: 20.0000 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1046 ASN C1046 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.193877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.112050 restraints weight = 37853.034| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.84 r_work: 0.3212 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 29600 Z= 0.093 Angle : 0.461 7.741 40112 Z= 0.233 Chirality : 0.039 0.129 4500 Planarity : 0.003 0.036 5092 Dihedral : 5.598 83.957 4016 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.95 % Allowed : 12.17 % Favored : 86.88 % 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 are not related in a simple way. whole: 0.64 (0.15), residues: 3568 helix: 1.21 (0.13), residues: 1724 sheet: -0.19 (0.27), residues: 400 loop : -0.23 (0.17), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B1041 TYR 0.010 0.001 TYR C 439 PHE 0.031 0.001 PHE B 300 TRP 0.011 0.001 TRP C 514 HIS 0.003 0.000 HIS C 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.09 (29600) covalent geometry : angle 0.46124 / 0.23 (40112) hydrogen bonds : bond 0.02952 / 1.93 ( 1312) hydrogen bonds : angle 3.93974 / 2.81 ( 3576) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 1.199 Fit side-chains REVERT: A 388 GLU cc_start: 0.7647 (mp0) cc_final: 0.7141 (mp0) REVERT: A 494 THR cc_start: 0.8841 (OUTLIER) cc_final: 0.8572 (p) REVERT: A 905 ASP cc_start: 0.7797 (p0) cc_final: 0.7563 (p0) REVERT: B 388 GLU cc_start: 0.7641 (mp0) cc_final: 0.7131 (mp0) REVERT: B 494 THR cc_start: 0.8840 (OUTLIER) cc_final: 0.8572 (p) REVERT: C 388 GLU cc_start: 0.7629 (mp0) cc_final: 0.7114 (mp0) REVERT: C 494 THR cc_start: 0.8845 (OUTLIER) cc_final: 0.8574 (p) REVERT: D 388 GLU cc_start: 0.7639 (mp0) cc_final: 0.7129 (mp0) REVERT: D 494 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8573 (p) REVERT: D 905 ASP cc_start: 0.7800 (p0) cc_final: 0.7564 (p0) outliers start: 30 outliers final: 10 residues processed: 160 average time/residue: 0.5354 time to fit residues: 103.4109 Evaluate side-chains 144 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 935 SER Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 935 SER Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 927 VAL Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 927 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 170 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 320 optimal weight: 8.9990 chunk 102 optimal weight: 0.1980 chunk 152 optimal weight: 0.5980 chunk 329 optimal weight: 0.6980 chunk 290 optimal weight: 7.9990 chunk 198 optimal weight: 30.0000 chunk 297 optimal weight: 6.9990 chunk 156 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.191432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.114034 restraints weight = 37191.953| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.61 r_work: 0.3255 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 29600 Z= 0.088 Angle : 0.453 7.448 40112 Z= 0.228 Chirality : 0.039 0.127 4500 Planarity : 0.003 0.036 5092 Dihedral : 5.135 78.579 4016 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.70 % Allowed : 12.90 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.15), residues: 3568 helix: 1.30 (0.13), residues: 1732 sheet: -0.11 (0.27), residues: 408 loop : -0.14 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 970 TYR 0.007 0.001 TYR A1025 PHE 0.036 0.001 PHE D 300 TRP 0.010 0.001 TRP D 514 HIS 0.002 0.000 HIS C 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.09 (29600) covalent geometry : angle 0.45348 / 0.23 (40112) hydrogen bonds : bond 0.02756 / 1.81 ( 1312) hydrogen bonds : angle 3.82065 / 2.73 ( 3576) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 1.071 Fit side-chains REVERT: A 388 GLU cc_start: 0.7788 (mp0) cc_final: 0.7373 (mp0) REVERT: A 494 THR cc_start: 0.8882 (OUTLIER) cc_final: 0.8634 (p) REVERT: A 832 MET cc_start: 0.7256 (mpp) cc_final: 0.6921 (mmm) REVERT: A 905 ASP cc_start: 0.8129 (p0) cc_final: 0.7853 (p0) REVERT: B 388 GLU cc_start: 0.7784 (mp0) cc_final: 0.7366 (mp0) REVERT: B 494 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8607 (p) REVERT: B 832 MET cc_start: 0.7250 (mpp) cc_final: 0.6923 (mmm) REVERT: B 905 ASP cc_start: 0.8095 (p0) cc_final: 0.7840 (p0) REVERT: C 388 GLU cc_start: 0.7770 (mp0) cc_final: 0.7354 (mp0) REVERT: C 494 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8640 (p) REVERT: C 832 MET cc_start: 0.7255 (mpp) cc_final: 0.6925 (mmm) REVERT: C 905 ASP cc_start: 0.8109 (p0) cc_final: 0.7849 (p0) REVERT: D 388 GLU cc_start: 0.7784 (mp0) cc_final: 0.7365 (mp0) REVERT: D 494 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8640 (p) REVERT: D 832 MET cc_start: 0.7299 (mpp) cc_final: 0.6970 (mmm) REVERT: D 905 ASP cc_start: 0.8112 (p0) cc_final: 0.7838 (p0) outliers start: 22 outliers final: 10 residues processed: 150 average time/residue: 0.6180 time to fit residues: 111.6669 Evaluate side-chains 142 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 935 SER Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 935 SER Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 927 VAL Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 927 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 131 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 200 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 331 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 204 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.191028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.113455 restraints weight = 36995.493| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.60 r_work: 0.3249 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29600 Z= 0.097 Angle : 0.456 7.274 40112 Z= 0.229 Chirality : 0.039 0.130 4500 Planarity : 0.003 0.035 5092 Dihedral : 4.973 74.005 4016 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.60 % Allowed : 13.25 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.15), residues: 3568 helix: 1.31 (0.13), residues: 1736 sheet: 0.03 (0.27), residues: 400 loop : -0.09 (0.17), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 503 TYR 0.014 0.001 TYR D1064 PHE 0.032 0.001 PHE A 300 TRP 0.009 0.001 TRP C 514 HIS 0.002 0.000 HIS C 771 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (29600) covalent geometry : angle 0.45598 / 0.23 (40112) hydrogen bonds : bond 0.02877 / 1.88 ( 1312) hydrogen bonds : angle 3.80155 / 2.72 ( 3576) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7136 Ramachandran restraints generated. 3568 Oldfield, 0 Emsley, 3568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 1.109 Fit side-chains REVERT: A 388 GLU cc_start: 0.7811 (mp0) cc_final: 0.7413 (mp0) REVERT: A 494 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8633 (p) REVERT: A 905 ASP cc_start: 0.8075 (p0) cc_final: 0.7831 (p0) REVERT: B 388 GLU cc_start: 0.7806 (mp0) cc_final: 0.7406 (mp0) REVERT: B 494 THR cc_start: 0.8905 (OUTLIER) cc_final: 0.8631 (p) REVERT: B 905 ASP cc_start: 0.8044 (p0) cc_final: 0.7816 (p0) REVERT: C 388 GLU cc_start: 0.7804 (mp0) cc_final: 0.7405 (mp0) REVERT: C 494 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8633 (p) REVERT: C 905 ASP cc_start: 0.8057 (p0) cc_final: 0.7819 (p0) REVERT: D 388 GLU cc_start: 0.7808 (mp0) cc_final: 0.7408 (mp0) REVERT: D 494 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8633 (p) REVERT: D 905 ASP cc_start: 0.8059 (p0) cc_final: 0.7813 (p0) outliers start: 19 outliers final: 11 residues processed: 145 average time/residue: 0.6440 time to fit residues: 111.4530 Evaluate side-chains 145 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 935 SER Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 927 VAL Chi-restraints excluded: chain C residue 935 SER Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 927 VAL Chi-restraints excluded: chain D residue 935 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 235 optimal weight: 30.0000 chunk 188 optimal weight: 20.0000 chunk 299 optimal weight: 0.9980 chunk 205 optimal weight: 6.9990 chunk 228 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 275 optimal weight: 9.9990 chunk 90 optimal weight: 110.0000 chunk 102 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1046 ASN B1046 ASN C1046 ASN D1046 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.189323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.111079 restraints weight = 37187.273| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.58 r_work: 0.3215 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29600 Z= 0.153 Angle : 0.514 7.607 40112 Z= 0.258 Chirality : 0.041 0.133 4500 Planarity : 0.004 0.048 5092 Dihedral : 4.982 69.507 4016 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.98 % Allowed : 12.96 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.15), residues: 3568 helix: 1.30 (0.13), residues: 1712 sheet: -0.11 (0.27), residues: 400 loop : -0.09 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 757 TYR 0.011 0.001 TYR A1025 PHE 0.036 0.001 PHE A 300 TRP 0.008 0.001 TRP A 391 HIS 0.004 0.001 HIS D 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.15 (29600) covalent geometry : angle 0.51383 / 0.26 (40112) hydrogen bonds : bond 0.03456 / 2.25 ( 1312) hydrogen bonds : angle 3.97909 / 2.86 ( 3576) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11765.06 seconds wall clock time: 200 minutes 11.96 seconds (12011.96 seconds total)