Starting phenix.real_space_refine on Fri Mar 6 07:11:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rjt_24490/03_2026/7rjt_24490.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rjt_24490/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7rjt_24490/03_2026/7rjt_24490.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rjt_24490/03_2026/7rjt_24490.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rjt_24490/03_2026/7rjt_24490.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rjt_24490/03_2026/7rjt_24490.map" } 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): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 161 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: 161 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: 161 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: 161 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: 6.46, per 1000 atoms: 0.22 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: 2.40 Conformation dependent library (CDL) restraints added in 1.4 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: 1.14 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: 6.46 Time building geometry restraints manager: 3.26 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: 15862 17.48 - 34.96: 1306 34.96 - 52.44: 260 52.44 - 69.92: 96 69.92 - 87.40: 16 Dihedral angle restraints: 17540 sinusoidal: 7008 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 17537 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: 1.740 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: 0.040 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 27.790 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 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 : 14.146 87.397 10732 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 covalent geometry : bond 0.00531 (29600) covalent geometry : angle 0.59063 (40112) hydrogen bonds : bond 0.14404 ( 1312) hydrogen bonds : angle 5.07860 ( 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 : 0.969 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.7061 time to fit residues: 134.8674 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 : 1.042 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 438 ASN D 897 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.188771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.109278 restraints weight = 36915.436| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.63 r_work: 0.3200 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 29600 Z= 0.204 Angle : 0.560 7.085 40112 Z= 0.281 Chirality : 0.044 0.181 4500 Planarity : 0.004 0.037 5092 Dihedral : 8.265 81.403 4024 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.02 % Allowed : 5.78 % Favored : 93.20 % 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: 0.57 (0.15), residues: 3568 helix: 1.05 (0.13), residues: 1628 sheet: -0.50 (0.27), residues: 404 loop : 0.05 (0.17), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 757 TYR 0.036 0.002 TYR C1025 PHE 0.013 0.001 PHE C 500 TRP 0.010 0.001 TRP B 514 HIS 0.007 0.001 HIS C 333 Details of bonding type rmsd covalent geometry : bond 0.00505 (29600) covalent geometry : angle 0.55958 (40112) hydrogen bonds : bond 0.04314 ( 1312) hydrogen bonds : angle 4.36050 ( 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 184 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 1.059 Fit side-chains REVERT: A 526 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7786 (ttp) REVERT: B 526 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7790 (ttp) REVERT: C 388 GLU cc_start: 0.7871 (mp0) cc_final: 0.7440 (mp0) REVERT: C 526 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7781 (ttp) REVERT: D 388 GLU cc_start: 0.7886 (mp0) cc_final: 0.7456 (mp0) REVERT: D 526 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7777 (ttp) outliers start: 32 outliers final: 8 residues processed: 164 average time/residue: 0.7839 time to fit residues: 147.3588 Evaluate side-chains 150 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 300 PHE Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 526 MET Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 526 MET Chi-restraints excluded: chain D residue 204 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: 0.9990 chunk 11 optimal weight: 50.0000 chunk 320 optimal weight: 0.0070 chunk 218 optimal weight: 0.6980 chunk 176 optimal weight: 0.8980 chunk 355 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 167 optimal weight: 0.6980 chunk 348 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 328 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 ASN B 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 = 0.4394 r_free = 0.4394 target = 0.191948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.114044 restraints weight = 37032.651| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.58 r_work: 0.3258 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 29600 Z= 0.090 Angle : 0.465 8.181 40112 Z= 0.235 Chirality : 0.039 0.158 4500 Planarity : 0.003 0.037 5092 Dihedral : 7.509 83.853 4024 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.10 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: 0.65 (0.15), residues: 3568 helix: 1.09 (0.13), residues: 1708 sheet: -0.28 (0.27), residues: 404 loop : -0.00 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 982 TYR 0.015 0.001 TYR C1025 PHE 0.010 0.001 PHE D 107 TRP 0.008 0.001 TRP C 514 HIS 0.002 0.000 HIS D 771 Details of bonding type rmsd covalent geometry : bond 0.00191 (29600) covalent geometry : angle 0.46464 (40112) hydrogen bonds : bond 0.03042 ( 1312) hydrogen bonds : angle 4.08637 ( 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 146 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 1.056 Fit side-chains outliers start: 12 outliers final: 0 residues processed: 134 average time/residue: 0.6881 time to fit residues: 108.7785 Evaluate side-chains 135 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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: 10.0000 chunk 148 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 306 optimal weight: 5.9990 chunk 284 optimal weight: 0.7980 chunk 180 optimal weight: 120.0000 chunk 193 optimal weight: 10.0000 chunk 0 optimal weight: 120.0000 chunk 69 optimal weight: 0.8980 chunk 261 optimal weight: 4.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.188675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.109651 restraints weight = 36886.023| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.58 r_work: 0.3193 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1291 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= 0.200 Angle : 0.542 6.890 40112 Z= 0.271 Chirality : 0.043 0.138 4500 Planarity : 0.004 0.037 5092 Dihedral : 7.195 84.876 4024 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.83 % Allowed : 10.10 % 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: 0.64 (0.15), residues: 3568 helix: 1.17 (0.13), residues: 1656 sheet: -0.44 (0.27), residues: 400 loop : -0.04 (0.17), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 503 TYR 0.021 0.002 TYR B1025 PHE 0.012 0.001 PHE B 500 TRP 0.009 0.001 TRP B 514 HIS 0.007 0.001 HIS B 333 Details of bonding type rmsd covalent geometry : bond 0.00494 (29600) covalent geometry : angle 0.54199 (40112) hydrogen bonds : bond 0.04010 ( 1312) hydrogen bonds : angle 4.17321 ( 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 170 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 1.004 Fit side-chains REVERT: A 388 GLU cc_start: 0.7853 (mp0) cc_final: 0.7368 (mp0) REVERT: A 494 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8700 (p) REVERT: B 388 GLU cc_start: 0.7853 (mp0) cc_final: 0.7369 (mp0) REVERT: B 494 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8704 (p) REVERT: C 388 GLU cc_start: 0.7842 (mp0) cc_final: 0.7357 (mp0) REVERT: C 494 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8702 (p) REVERT: D 388 GLU cc_start: 0.7846 (mp0) cc_final: 0.7363 (mp0) REVERT: D 494 THR cc_start: 0.8990 (OUTLIER) cc_final: 0.8702 (p) outliers start: 26 outliers final: 4 residues processed: 158 average time/residue: 0.6175 time to fit residues: 116.6806 Evaluate side-chains 143 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 PHE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain D residue 300 PHE 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: 0.7980 chunk 69 optimal weight: 0.9990 chunk 198 optimal weight: 30.0000 chunk 227 optimal weight: 10.0000 chunk 256 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 195 optimal weight: 0.9990 chunk 352 optimal weight: 0.0870 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.193867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.118564 restraints weight = 37811.735| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 3.70 r_work: 0.3167 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1330 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= 0.109 Angle : 0.469 7.968 40112 Z= 0.237 Chirality : 0.040 0.132 4500 Planarity : 0.003 0.036 5092 Dihedral : 6.635 85.425 4024 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.51 % Allowed : 11.34 % Favored : 88.15 % 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: 0.52 (0.15), residues: 3568 helix: 1.12 (0.13), residues: 1724 sheet: -0.41 (0.27), residues: 408 loop : -0.26 (0.17), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 982 TYR 0.011 0.001 TYR C1025 PHE 0.007 0.001 PHE C1010 TRP 0.009 0.001 TRP C 514 HIS 0.002 0.001 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00256 (29600) covalent geometry : angle 0.46922 (40112) hydrogen bonds : bond 0.03085 ( 1312) hydrogen bonds : angle 4.01400 ( 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 151 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.999 Fit side-chains REVERT: A 388 GLU cc_start: 0.7418 (mp0) cc_final: 0.6865 (mp0) REVERT: B 388 GLU cc_start: 0.7407 (mp0) cc_final: 0.6847 (mp0) REVERT: C 388 GLU cc_start: 0.7395 (mp0) cc_final: 0.6834 (mp0) REVERT: D 388 GLU cc_start: 0.7415 (mp0) cc_final: 0.6859 (mp0) outliers start: 16 outliers final: 3 residues processed: 147 average time/residue: 0.6083 time to fit residues: 106.7073 Evaluate side-chains 135 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 132 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 ASN Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain C residue 438 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 185 optimal weight: 30.0000 chunk 54 optimal weight: 10.0000 chunk 159 optimal weight: 0.7980 chunk 320 optimal weight: 7.9990 chunk 246 optimal weight: 0.2980 chunk 120 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 207 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 HIS B 453 HIS C 453 HIS D 453 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.191611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.108591 restraints weight = 37765.174| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.83 r_work: 0.3160 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1486 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= 0.203 Angle : 0.537 6.924 40112 Z= 0.269 Chirality : 0.043 0.136 4500 Planarity : 0.004 0.036 5092 Dihedral : 6.391 86.266 4024 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.89 % Allowed : 11.79 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.15), residues: 3568 helix: 1.24 (0.13), residues: 1656 sheet: -0.43 (0.27), residues: 400 loop : -0.05 (0.17), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 503 TYR 0.015 0.001 TYR A1025 PHE 0.024 0.001 PHE B 300 TRP 0.009 0.001 TRP C 514 HIS 0.006 0.001 HIS D 333 Details of bonding type rmsd covalent geometry : bond 0.00505 (29600) covalent geometry : angle 0.53676 (40112) hydrogen bonds : bond 0.03887 ( 1312) hydrogen bonds : angle 4.08775 ( 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 160 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.999 Fit side-chains REVERT: A 388 GLU cc_start: 0.7752 (mp0) cc_final: 0.7227 (mp0) REVERT: A 494 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8635 (p) REVERT: B 388 GLU cc_start: 0.7756 (mp0) cc_final: 0.7229 (mp0) REVERT: B 494 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8637 (p) REVERT: B 905 ASP cc_start: 0.7446 (p0) cc_final: 0.7088 (p0) REVERT: C 300 PHE cc_start: 0.8139 (t80) cc_final: 0.7819 (m-80) REVERT: C 388 GLU cc_start: 0.7750 (mp0) cc_final: 0.7221 (mp0) REVERT: C 494 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8638 (p) REVERT: D 300 PHE cc_start: 0.8140 (t80) cc_final: 0.7821 (m-80) REVERT: D 388 GLU cc_start: 0.7753 (mp0) cc_final: 0.7224 (mp0) REVERT: D 494 THR cc_start: 0.8955 (OUTLIER) cc_final: 0.8639 (p) REVERT: D 905 ASP cc_start: 0.7462 (p0) cc_final: 0.7104 (p0) outliers start: 28 outliers final: 4 residues processed: 152 average time/residue: 0.5837 time to fit residues: 106.2857 Evaluate side-chains 139 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 522 THR 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: 8.9990 chunk 66 optimal weight: 1.9990 chunk 354 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 45 optimal weight: 0.5980 chunk 113 optimal weight: 10.0000 chunk 288 optimal weight: 30.0000 chunk 184 optimal weight: 8.9990 chunk 73 optimal weight: 0.3980 chunk 243 optimal weight: 0.9990 chunk 276 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.192303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.109593 restraints weight = 37788.274| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.84 r_work: 0.3179 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 29600 Z= 0.152 Angle : 0.501 7.616 40112 Z= 0.252 Chirality : 0.041 0.133 4500 Planarity : 0.003 0.036 5092 Dihedral : 6.067 86.900 4024 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.08 % Allowed : 12.17 % Favored : 86.75 % 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: 0.70 (0.15), residues: 3568 helix: 1.28 (0.13), residues: 1656 sheet: -0.45 (0.27), residues: 408 loop : -0.07 (0.17), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 503 TYR 0.011 0.001 TYR A1025 PHE 0.009 0.001 PHE C 500 TRP 0.010 0.001 TRP C 514 HIS 0.004 0.001 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00374 (29600) covalent geometry : angle 0.50087 (40112) hydrogen bonds : bond 0.03484 ( 1312) hydrogen bonds : angle 4.04289 ( 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 163 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.904 Fit side-chains REVERT: A 300 PHE cc_start: 0.6725 (t80) cc_final: 0.6211 (t80) REVERT: A 388 GLU cc_start: 0.7757 (mp0) cc_final: 0.7231 (mp0) REVERT: A 494 THR cc_start: 0.8907 (OUTLIER) cc_final: 0.8608 (p) REVERT: B 300 PHE cc_start: 0.6719 (t80) cc_final: 0.6172 (t80) REVERT: B 388 GLU cc_start: 0.7757 (mp0) cc_final: 0.7227 (mp0) REVERT: B 494 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8608 (p) REVERT: C 388 GLU cc_start: 0.7748 (mp0) cc_final: 0.7215 (mp0) REVERT: C 494 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8608 (p) REVERT: D 388 GLU cc_start: 0.7751 (mp0) cc_final: 0.7221 (mp0) REVERT: D 494 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8611 (p) outliers start: 34 outliers final: 8 residues processed: 157 average time/residue: 0.6418 time to fit residues: 120.4300 Evaluate side-chains 140 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 927 VAL Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 494 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 927 VAL Chi-restraints excluded: chain D residue 438 ASN Chi-restraints excluded: chain D residue 494 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: 9.9990 chunk 208 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 199 optimal weight: 30.0000 chunk 258 optimal weight: 0.5980 chunk 156 optimal weight: 0.6980 chunk 165 optimal weight: 0.9990 chunk 265 optimal weight: 6.9990 chunk 327 optimal weight: 0.0980 chunk 66 optimal weight: 0.8980 chunk 189 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.194610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.113059 restraints weight = 37699.305| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.85 r_work: 0.3232 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 29600 Z= 0.088 Angle : 0.452 7.690 40112 Z= 0.228 Chirality : 0.038 0.125 4500 Planarity : 0.003 0.036 5092 Dihedral : 5.576 87.438 4024 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.95 % Allowed : 12.87 % Favored : 86.18 % 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: 1.24 (0.13), residues: 1728 sheet: -0.23 (0.27), residues: 408 loop : -0.18 (0.17), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 970 TYR 0.008 0.001 TYR B1025 PHE 0.027 0.001 PHE C 300 TRP 0.011 0.001 TRP D 514 HIS 0.002 0.000 HIS C 771 Details of bonding type rmsd covalent geometry : bond 0.00194 (29600) covalent geometry : angle 0.45228 (40112) hydrogen bonds : bond 0.02763 ( 1312) hydrogen bonds : angle 3.87135 ( 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 : 1.129 Fit side-chains REVERT: A 300 PHE cc_start: 0.6766 (t80) cc_final: 0.6330 (t80) REVERT: A 388 GLU cc_start: 0.7655 (mp0) cc_final: 0.7147 (mp0) REVERT: A 494 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8538 (p) REVERT: B 300 PHE cc_start: 0.6767 (t80) cc_final: 0.6317 (t80) REVERT: B 388 GLU cc_start: 0.7632 (mp0) cc_final: 0.7121 (mp0) REVERT: B 494 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8540 (p) REVERT: C 388 GLU cc_start: 0.7622 (mp0) cc_final: 0.7110 (mp0) REVERT: C 494 THR cc_start: 0.8799 (OUTLIER) cc_final: 0.8545 (p) REVERT: C 905 ASP cc_start: 0.7977 (p0) cc_final: 0.7658 (p0) REVERT: D 388 GLU cc_start: 0.7647 (mp0) cc_final: 0.7135 (mp0) REVERT: D 494 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8544 (p) outliers start: 30 outliers final: 12 residues processed: 158 average time/residue: 0.6176 time to fit residues: 116.8843 Evaluate side-chains 143 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 927 VAL Chi-restraints excluded: chain A residue 935 SER Chi-restraints excluded: chain B residue 438 ASN 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 438 ASN 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 438 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 170 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 320 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 152 optimal weight: 1.9990 chunk 329 optimal weight: 3.9990 chunk 290 optimal weight: 8.9990 chunk 198 optimal weight: 30.0000 chunk 297 optimal weight: 7.9990 chunk 156 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4363 r_free = 0.4363 target = 0.189190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.110668 restraints weight = 36998.314| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.59 r_work: 0.3213 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 29600 Z= 0.154 Angle : 0.510 7.076 40112 Z= 0.257 Chirality : 0.041 0.132 4500 Planarity : 0.003 0.035 5092 Dihedral : 5.551 88.096 4024 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.02 % Allowed : 13.09 % Favored : 85.90 % 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: 0.73 (0.15), residues: 3568 helix: 1.30 (0.13), residues: 1700 sheet: -0.26 (0.27), residues: 408 loop : -0.16 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 503 TYR 0.014 0.001 TYR B1064 PHE 0.024 0.001 PHE D 300 TRP 0.008 0.001 TRP D 391 HIS 0.004 0.001 HIS D 333 Details of bonding type rmsd covalent geometry : bond 0.00380 (29600) covalent geometry : angle 0.51043 (40112) hydrogen bonds : bond 0.03477 ( 1312) hydrogen bonds : angle 3.99038 ( 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 165 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 1.121 Fit side-chains REVERT: A 300 PHE cc_start: 0.6808 (t80) cc_final: 0.6370 (t80) REVERT: A 304 PHE cc_start: 0.5442 (t80) cc_final: 0.5213 (t80) REVERT: A 388 GLU cc_start: 0.7864 (mp0) cc_final: 0.7433 (mp0) REVERT: A 494 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8683 (p) REVERT: A 706 ARG cc_start: 0.7886 (mmt180) cc_final: 0.7463 (mmt180) REVERT: A 832 MET cc_start: 0.7343 (mpp) cc_final: 0.7022 (mmm) REVERT: A 905 ASP cc_start: 0.7828 (p0) cc_final: 0.7415 (p0) REVERT: B 300 PHE cc_start: 0.6805 (t80) cc_final: 0.6363 (t80) REVERT: B 388 GLU cc_start: 0.7863 (mp0) cc_final: 0.7430 (mp0) REVERT: B 494 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8684 (p) REVERT: B 706 ARG cc_start: 0.7890 (mmt180) cc_final: 0.7466 (mmt180) REVERT: B 832 MET cc_start: 0.7337 (mpp) cc_final: 0.7015 (mmm) REVERT: B 905 ASP cc_start: 0.7834 (p0) cc_final: 0.7413 (p0) REVERT: C 388 GLU cc_start: 0.7856 (mp0) cc_final: 0.7421 (mp0) REVERT: C 494 THR cc_start: 0.8973 (OUTLIER) cc_final: 0.8684 (p) REVERT: C 706 ARG cc_start: 0.7885 (mmt180) cc_final: 0.7461 (mmt180) REVERT: C 832 MET cc_start: 0.7348 (mpp) cc_final: 0.7026 (mmm) REVERT: C 905 ASP cc_start: 0.8018 (p0) cc_final: 0.7656 (p0) REVERT: D 388 GLU cc_start: 0.7852 (mp0) cc_final: 0.7418 (mp0) REVERT: D 494 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8682 (p) REVERT: D 706 ARG cc_start: 0.7888 (mmt180) cc_final: 0.7465 (mmt180) REVERT: D 832 MET cc_start: 0.7358 (mpp) cc_final: 0.7038 (mmm) REVERT: D 905 ASP cc_start: 0.7802 (p0) cc_final: 0.7393 (p0) outliers start: 32 outliers final: 12 residues processed: 161 average time/residue: 0.6471 time to fit residues: 123.5293 Evaluate side-chains 148 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 927 VAL Chi-restraints excluded: chain A residue 935 SER Chi-restraints excluded: chain B residue 438 ASN 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 438 ASN 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 438 ASN 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 131 optimal weight: 6.9990 chunk 154 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 200 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 331 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 204 optimal weight: 0.6980 chunk 153 optimal weight: 0.0470 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4383 r_free = 0.4383 target = 0.191196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.113646 restraints weight = 36906.928| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.57 r_work: 0.3257 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1655 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= 0.089 Angle : 0.457 7.345 40112 Z= 0.231 Chirality : 0.039 0.128 4500 Planarity : 0.003 0.036 5092 Dihedral : 5.364 88.490 4024 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.51 % Allowed : 13.53 % Favored : 85.96 % 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: 0.77 (0.15), residues: 3568 helix: 1.31 (0.13), residues: 1728 sheet: -0.14 (0.27), residues: 408 loop : -0.15 (0.17), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 503 TYR 0.008 0.001 TYR C1025 PHE 0.024 0.001 PHE D 300 TRP 0.011 0.001 TRP A 514 HIS 0.002 0.000 HIS C 771 Details of bonding type rmsd covalent geometry : bond 0.00200 (29600) covalent geometry : angle 0.45719 (40112) hydrogen bonds : bond 0.02817 ( 1312) hydrogen bonds : angle 3.85116 ( 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 150 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 1.009 Fit side-chains REVERT: A 388 GLU cc_start: 0.7782 (mp0) cc_final: 0.7363 (mp0) REVERT: A 494 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8623 (p) REVERT: A 905 ASP cc_start: 0.8027 (p0) cc_final: 0.7814 (p0) REVERT: B 388 GLU cc_start: 0.7775 (mp0) cc_final: 0.7353 (mp0) REVERT: B 494 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8625 (p) REVERT: B 905 ASP cc_start: 0.8017 (p0) cc_final: 0.7809 (p0) REVERT: C 388 GLU cc_start: 0.7768 (mp0) cc_final: 0.7347 (mp0) REVERT: C 494 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8627 (p) REVERT: D 388 GLU cc_start: 0.7773 (mp0) cc_final: 0.7354 (mp0) REVERT: D 494 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8622 (p) REVERT: D 905 ASP cc_start: 0.8026 (p0) cc_final: 0.7824 (p0) outliers start: 16 outliers final: 8 residues processed: 150 average time/residue: 0.6234 time to fit residues: 111.1113 Evaluate side-chains 143 residues out of total 3148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 927 VAL Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 494 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 927 VAL Chi-restraints excluded: chain D residue 438 ASN 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 235 optimal weight: 30.0000 chunk 188 optimal weight: 7.9990 chunk 299 optimal weight: 4.9990 chunk 205 optimal weight: 7.9990 chunk 228 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 275 optimal weight: 8.9990 chunk 90 optimal weight: 100.0000 chunk 102 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1046 ASN C1046 ASN D1046 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.188289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.109542 restraints weight = 37083.018| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.58 r_work: 0.3197 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 29600 Z= 0.200 Angle : 0.534 7.279 40112 Z= 0.267 Chirality : 0.042 0.133 4500 Planarity : 0.004 0.051 5092 Dihedral : 5.491 89.260 4024 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.89 % Allowed : 13.31 % Favored : 85.80 % 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: 0.88 (0.15), residues: 3568 helix: 1.40 (0.13), residues: 1656 sheet: -0.17 (0.27), residues: 400 loop : 0.01 (0.17), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 757 TYR 0.016 0.001 TYR A1064 PHE 0.036 0.001 PHE D 300 TRP 0.009 0.001 TRP A 391 HIS 0.006 0.001 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00498 (29600) covalent geometry : angle 0.53377 (40112) hydrogen bonds : bond 0.03815 ( 1312) hydrogen bonds : angle 4.00501 ( 3576) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12935.89 seconds wall clock time: 219 minutes 57.29 seconds (13197.29 seconds total)