Starting phenix.real_space_refine on Mon Aug 25 17:09:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b94_44368/08_2025/9b94_44368.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b94_44368/08_2025/9b94_44368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b94_44368/08_2025/9b94_44368.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b94_44368/08_2025/9b94_44368.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b94_44368/08_2025/9b94_44368.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b94_44368/08_2025/9b94_44368.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 144 5.16 5 C 19128 2.51 5 N 5208 2.21 5 O 5032 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29516 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7378 Classifications: {'peptide': 966} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 42, 'TRANS': 923} Chain breaks: 10 Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 388 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 13, 'GLN:plan1': 4, 'ARG:plan': 12, 'ASP:plan': 15, 'HIS:plan': 2, 'PHE:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 223 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 8.87, per 1000 atoms: 0.30 Number of scatterers: 29516 At special positions: 0 Unit cell: (163.116, 163.116, 158.976, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 144 16.00 O 5032 8.00 N 5208 7.00 C 19128 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: 3.09 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 1.2 microseconds 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7168 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 16 sheets defined 67.5% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 9 through 15 removed outlier: 3.989A pdb=" N LYS A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 108 removed outlier: 3.904A pdb=" N VAL A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 141 Processing helix chain 'A' and resid 141 through 150 Processing helix chain 'A' and resid 160 through 174 removed outlier: 3.688A pdb=" N HIS A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 201 Processing helix chain 'A' and resid 246 through 259 Processing helix chain 'A' and resid 264 through 268 removed outlier: 3.993A pdb=" N GLY A 268 " --> pdb=" O GLY A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 Processing helix chain 'A' and resid 308 through 317 Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 344 through 357 removed outlier: 3.976A pdb=" N GLN A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 386 removed outlier: 3.638A pdb=" N ILE A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 405 through 415 removed outlier: 4.012A pdb=" N ALA A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 435 removed outlier: 3.547A pdb=" N LEU A 425 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 428 " --> pdb=" O HIS A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 447 Processing helix chain 'A' and resid 456 through 466 Processing helix chain 'A' and resid 471 through 480 Processing helix chain 'A' and resid 502 through 512 removed outlier: 3.890A pdb=" N VAL A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 584 through 602 Processing helix chain 'A' and resid 605 through 634 Processing helix chain 'A' and resid 638 through 643 removed outlier: 3.551A pdb=" N LEU A 643 " --> pdb=" O ALA A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 663 through 669 removed outlier: 3.591A pdb=" N GLN A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 681 Processing helix chain 'A' and resid 689 through 699 Processing helix chain 'A' and resid 700 through 705 Processing helix chain 'A' and resid 767 through 778 Processing helix chain 'A' and resid 778 through 803 Processing helix chain 'A' and resid 811 through 834 Processing helix chain 'A' and resid 852 through 861 Processing helix chain 'A' and resid 862 through 884 Processing helix chain 'A' and resid 887 through 905 removed outlier: 3.625A pdb=" N MET A 900 " --> pdb=" O CYS A 896 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG A 905 " --> pdb=" O VAL A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 912 Processing helix chain 'A' and resid 915 through 926 removed outlier: 3.759A pdb=" N LYS A 919 " --> pdb=" O GLN A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 953 Processing helix chain 'A' and resid 958 through 974 removed outlier: 4.829A pdb=" N ARG A 969 " --> pdb=" O ARG A 965 " (cutoff:3.500A) Proline residue: A 970 - end of helix removed outlier: 3.644A pdb=" N ILE A 974 " --> pdb=" O PRO A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 983 Processing helix chain 'A' and resid 984 through 988 Processing helix chain 'A' and resid 1016 through 1033 removed outlier: 3.780A pdb=" N VAL A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1050 Processing helix chain 'A' and resid 1050 through 1071 removed outlier: 4.348A pdb=" N TYR A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1088 removed outlier: 4.000A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG A1086 " --> pdb=" O ILE A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1142 Processing helix chain 'A' and resid 1143 through 1167 removed outlier: 3.519A pdb=" N GLU A1167 " --> pdb=" O GLY A1163 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 15 removed outlier: 3.989A pdb=" N LYS B 13 " --> pdb=" O SER B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 108 removed outlier: 3.903A pdb=" N VAL B 102 " --> pdb=" O ASP B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 141 Processing helix chain 'B' and resid 141 through 150 Processing helix chain 'B' and resid 160 through 174 removed outlier: 3.688A pdb=" N HIS B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 201 Processing helix chain 'B' and resid 246 through 259 Processing helix chain 'B' and resid 264 through 268 removed outlier: 3.993A pdb=" N GLY B 268 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 294 Processing helix chain 'B' and resid 308 through 317 Processing helix chain 'B' and resid 329 through 337 Processing helix chain 'B' and resid 344 through 357 removed outlier: 3.976A pdb=" N GLN B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 386 removed outlier: 3.638A pdb=" N ILE B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 405 through 415 removed outlier: 4.012A pdb=" N ALA B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 435 removed outlier: 3.548A pdb=" N LEU B 425 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER B 428 " --> pdb=" O HIS B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 447 Processing helix chain 'B' and resid 456 through 466 Processing helix chain 'B' and resid 471 through 480 Processing helix chain 'B' and resid 502 through 512 removed outlier: 3.890A pdb=" N VAL B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 570 Processing helix chain 'B' and resid 571 through 581 Processing helix chain 'B' and resid 584 through 602 Processing helix chain 'B' and resid 605 through 634 Processing helix chain 'B' and resid 638 through 643 removed outlier: 3.550A pdb=" N LEU B 643 " --> pdb=" O ALA B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 663 through 669 removed outlier: 3.590A pdb=" N GLN B 669 " --> pdb=" O ALA B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 681 Processing helix chain 'B' and resid 689 through 699 Processing helix chain 'B' and resid 700 through 705 Processing helix chain 'B' and resid 767 through 778 Processing helix chain 'B' and resid 778 through 803 Processing helix chain 'B' and resid 811 through 834 Processing helix chain 'B' and resid 852 through 861 Processing helix chain 'B' and resid 862 through 884 Processing helix chain 'B' and resid 887 through 905 removed outlier: 3.626A pdb=" N MET B 900 " --> pdb=" O CYS B 896 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG B 905 " --> pdb=" O VAL B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 912 Processing helix chain 'B' and resid 915 through 926 removed outlier: 3.759A pdb=" N LYS B 919 " --> pdb=" O GLN B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 953 Processing helix chain 'B' and resid 958 through 974 removed outlier: 4.829A pdb=" N ARG B 969 " --> pdb=" O ARG B 965 " (cutoff:3.500A) Proline residue: B 970 - end of helix removed outlier: 3.644A pdb=" N ILE B 974 " --> pdb=" O PRO B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 983 Processing helix chain 'B' and resid 984 through 988 Processing helix chain 'B' and resid 1016 through 1033 removed outlier: 3.781A pdb=" N VAL B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1050 Processing helix chain 'B' and resid 1050 through 1071 removed outlier: 4.348A pdb=" N TYR B1063 " --> pdb=" O LYS B1059 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG B1064 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing helix chain 'B' and resid 1079 through 1088 removed outlier: 4.000A pdb=" N SER B1083 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG B1086 " --> pdb=" O ILE B1082 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1142 Processing helix chain 'B' and resid 1143 through 1167 removed outlier: 3.519A pdb=" N GLU B1167 " --> pdb=" O GLY B1163 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 15 removed outlier: 3.990A pdb=" N LYS C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 108 removed outlier: 3.903A pdb=" N VAL C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 141 Processing helix chain 'C' and resid 141 through 150 Processing helix chain 'C' and resid 160 through 174 removed outlier: 3.687A pdb=" N HIS C 165 " --> pdb=" O GLY C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 201 Processing helix chain 'C' and resid 246 through 259 Processing helix chain 'C' and resid 264 through 268 removed outlier: 3.993A pdb=" N GLY C 268 " --> pdb=" O GLY C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 294 Processing helix chain 'C' and resid 308 through 317 Processing helix chain 'C' and resid 329 through 337 Processing helix chain 'C' and resid 344 through 357 removed outlier: 3.976A pdb=" N GLN C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 386 removed outlier: 3.638A pdb=" N ILE C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 405 through 415 removed outlier: 4.011A pdb=" N ALA C 409 " --> pdb=" O ARG C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 435 removed outlier: 3.547A pdb=" N LEU C 425 " --> pdb=" O ARG C 421 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER C 428 " --> pdb=" O HIS C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 447 Processing helix chain 'C' and resid 456 through 466 Processing helix chain 'C' and resid 471 through 480 Processing helix chain 'C' and resid 502 through 512 removed outlier: 3.889A pdb=" N VAL C 506 " --> pdb=" O ASP C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 570 Processing helix chain 'C' and resid 571 through 581 Processing helix chain 'C' and resid 584 through 602 Processing helix chain 'C' and resid 605 through 634 Processing helix chain 'C' and resid 638 through 643 removed outlier: 3.551A pdb=" N LEU C 643 " --> pdb=" O ALA C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 663 through 669 removed outlier: 3.591A pdb=" N GLN C 669 " --> pdb=" O ALA C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 681 Processing helix chain 'C' and resid 689 through 699 Processing helix chain 'C' and resid 700 through 705 Processing helix chain 'C' and resid 767 through 778 Processing helix chain 'C' and resid 778 through 803 Processing helix chain 'C' and resid 811 through 834 Processing helix chain 'C' and resid 852 through 861 Processing helix chain 'C' and resid 862 through 884 Processing helix chain 'C' and resid 887 through 905 removed outlier: 3.625A pdb=" N MET C 900 " --> pdb=" O CYS C 896 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG C 905 " --> pdb=" O VAL C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 906 through 912 Processing helix chain 'C' and resid 915 through 926 removed outlier: 3.759A pdb=" N LYS C 919 " --> pdb=" O GLN C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 953 Processing helix chain 'C' and resid 958 through 974 removed outlier: 4.829A pdb=" N ARG C 969 " --> pdb=" O ARG C 965 " (cutoff:3.500A) Proline residue: C 970 - end of helix removed outlier: 3.644A pdb=" N ILE C 974 " --> pdb=" O PRO C 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 983 Processing helix chain 'C' and resid 984 through 988 Processing helix chain 'C' and resid 1016 through 1033 removed outlier: 3.780A pdb=" N VAL C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1050 Processing helix chain 'C' and resid 1050 through 1071 removed outlier: 4.348A pdb=" N TYR C1063 " --> pdb=" O LYS C1059 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG C1064 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing helix chain 'C' and resid 1079 through 1088 removed outlier: 4.000A pdb=" N SER C1083 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG C1086 " --> pdb=" O ILE C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1142 Processing helix chain 'C' and resid 1143 through 1167 removed outlier: 3.519A pdb=" N GLU C1167 " --> pdb=" O GLY C1163 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 15 removed outlier: 3.989A pdb=" N LYS D 13 " --> pdb=" O SER D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 108 removed outlier: 3.904A pdb=" N VAL D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 141 Processing helix chain 'D' and resid 141 through 150 Processing helix chain 'D' and resid 160 through 174 removed outlier: 3.688A pdb=" N HIS D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 201 Processing helix chain 'D' and resid 246 through 259 Processing helix chain 'D' and resid 264 through 268 removed outlier: 3.992A pdb=" N GLY D 268 " --> pdb=" O GLY D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 294 Processing helix chain 'D' and resid 308 through 317 Processing helix chain 'D' and resid 329 through 337 Processing helix chain 'D' and resid 344 through 357 removed outlier: 3.977A pdb=" N GLN D 348 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG D 357 " --> pdb=" O ARG D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 removed outlier: 3.637A pdb=" N ILE D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 403 Processing helix chain 'D' and resid 405 through 415 removed outlier: 4.011A pdb=" N ALA D 409 " --> pdb=" O ARG D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 435 removed outlier: 3.547A pdb=" N LEU D 425 " --> pdb=" O ARG D 421 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER D 428 " --> pdb=" O HIS D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 447 Processing helix chain 'D' and resid 456 through 466 Processing helix chain 'D' and resid 471 through 480 Processing helix chain 'D' and resid 502 through 512 removed outlier: 3.889A pdb=" N VAL D 506 " --> pdb=" O ASP D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 570 Processing helix chain 'D' and resid 571 through 581 Processing helix chain 'D' and resid 584 through 602 Processing helix chain 'D' and resid 605 through 634 Processing helix chain 'D' and resid 638 through 643 removed outlier: 3.551A pdb=" N LEU D 643 " --> pdb=" O ALA D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 663 through 669 removed outlier: 3.590A pdb=" N GLN D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 681 Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 700 through 705 Processing helix chain 'D' and resid 767 through 778 Processing helix chain 'D' and resid 778 through 803 Processing helix chain 'D' and resid 811 through 834 Processing helix chain 'D' and resid 852 through 861 Processing helix chain 'D' and resid 862 through 884 Processing helix chain 'D' and resid 887 through 905 removed outlier: 3.625A pdb=" N MET D 900 " --> pdb=" O CYS D 896 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG D 905 " --> pdb=" O VAL D 901 " (cutoff:3.500A) Processing helix chain 'D' and resid 906 through 912 Processing helix chain 'D' and resid 915 through 926 removed outlier: 3.758A pdb=" N LYS D 919 " --> pdb=" O GLN D 915 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 953 Processing helix chain 'D' and resid 958 through 974 removed outlier: 4.829A pdb=" N ARG D 969 " --> pdb=" O ARG D 965 " (cutoff:3.500A) Proline residue: D 970 - end of helix removed outlier: 3.645A pdb=" N ILE D 974 " --> pdb=" O PRO D 970 " (cutoff:3.500A) Processing helix chain 'D' and resid 979 through 983 Processing helix chain 'D' and resid 984 through 988 Processing helix chain 'D' and resid 1016 through 1033 removed outlier: 3.780A pdb=" N VAL D1020 " --> pdb=" O ALA D1016 " (cutoff:3.500A) Processing helix chain 'D' and resid 1033 through 1050 Processing helix chain 'D' and resid 1050 through 1071 removed outlier: 4.348A pdb=" N TYR D1063 " --> pdb=" O LYS D1059 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG D1064 " --> pdb=" O ALA D1060 " (cutoff:3.500A) Processing helix chain 'D' and resid 1079 through 1088 removed outlier: 4.000A pdb=" N SER D1083 " --> pdb=" O PHE D1079 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG D1086 " --> pdb=" O ILE D1082 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1142 Processing helix chain 'D' and resid 1143 through 1167 removed outlier: 3.518A pdb=" N GLU D1167 " --> pdb=" O GLY D1163 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 19 removed outlier: 3.851A pdb=" N THR A 68 " --> pdb=" O THR A 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 78 Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 94 removed outlier: 6.098A pdb=" N LEU A 93 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALA A 185 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE A 233 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY A 187 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL A 235 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA A 189 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE A 153 " --> pdb=" O MET A 186 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL A 188 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR A 155 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N LEU A 299 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU A 275 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL A 301 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU A 277 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 989 through 991 removed outlier: 4.025A pdb=" N GLU A 989 " --> pdb=" O HIS A1002 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP A1000 " --> pdb=" O SER A 991 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 19 removed outlier: 3.851A pdb=" N THR B 68 " --> pdb=" O THR B 19 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'B' and resid 92 through 94 removed outlier: 6.097A pdb=" N LEU B 93 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ALA B 185 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N PHE B 233 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY B 187 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL B 235 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA B 189 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE B 153 " --> pdb=" O MET B 186 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL B 188 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR B 155 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N LEU B 299 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU B 275 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL B 301 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU B 277 " --> pdb=" O VAL B 301 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 989 through 991 removed outlier: 4.025A pdb=" N GLU B 989 " --> pdb=" O HIS B1002 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP B1000 " --> pdb=" O SER B 991 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 16 through 19 removed outlier: 3.851A pdb=" N THR C 68 " --> pdb=" O THR C 19 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 78 removed outlier: 3.969A pdb=" N GLY C 76 " --> pdb=" O PHE C 90 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 92 through 94 removed outlier: 6.098A pdb=" N LEU C 93 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALA C 185 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE C 233 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY C 187 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL C 235 " --> pdb=" O GLY C 187 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA C 189 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE C 153 " --> pdb=" O MET C 186 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL C 188 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR C 155 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N LEU C 299 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU C 275 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL C 301 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LEU C 277 " --> pdb=" O VAL C 301 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 989 through 991 removed outlier: 4.025A pdb=" N GLU C 989 " --> pdb=" O HIS C1002 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP C1000 " --> pdb=" O SER C 991 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 16 through 19 removed outlier: 3.852A pdb=" N THR D 68 " --> pdb=" O THR D 19 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 78 removed outlier: 3.969A pdb=" N GLY D 76 " --> pdb=" O PHE D 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 92 through 94 removed outlier: 6.097A pdb=" N LEU D 93 " --> pdb=" O ASP D 236 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ALA D 185 " --> pdb=" O ALA D 231 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE D 233 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY D 187 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL D 235 " --> pdb=" O GLY D 187 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA D 189 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE D 153 " --> pdb=" O MET D 186 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL D 188 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR D 155 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N LEU D 299 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU D 275 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL D 301 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LEU D 277 " --> pdb=" O VAL D 301 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 989 through 991 removed outlier: 4.025A pdb=" N GLU D 989 " --> pdb=" O HIS D1002 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TRP D1000 " --> pdb=" O SER D 991 " (cutoff:3.500A) 1830 hydrogen bonds defined for protein. 5298 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: 6.67 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9564 1.34 - 1.46: 7176 1.46 - 1.58: 13228 1.58 - 1.70: 0 1.70 - 1.82: 220 Bond restraints: 30188 Sorted by residual: bond pdb=" N ASP C 605 " pdb=" CA ASP C 605 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.21e-02 6.83e+03 8.29e+00 bond pdb=" N ASP A 605 " pdb=" CA ASP A 605 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.21e-02 6.83e+03 8.24e+00 bond pdb=" N ASP B 605 " pdb=" CA ASP B 605 " ideal model delta sigma weight residual 1.456 1.491 -0.034 1.21e-02 6.83e+03 8.08e+00 bond pdb=" N ASP D 605 " pdb=" CA ASP D 605 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.21e-02 6.83e+03 7.91e+00 bond pdb=" N GLU C 607 " pdb=" CA GLU C 607 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.61e+00 ... (remaining 30183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 39931 1.20 - 2.40: 837 2.40 - 3.60: 208 3.60 - 4.80: 57 4.80 - 6.00: 15 Bond angle restraints: 41048 Sorted by residual: angle pdb=" C THR D 21 " pdb=" CA THR D 21 " pdb=" CB THR D 21 " ideal model delta sigma weight residual 116.63 112.18 4.45 1.16e+00 7.43e-01 1.47e+01 angle pdb=" C THR A 21 " pdb=" CA THR A 21 " pdb=" CB THR A 21 " ideal model delta sigma weight residual 116.63 112.21 4.42 1.16e+00 7.43e-01 1.45e+01 angle pdb=" C THR C 21 " pdb=" CA THR C 21 " pdb=" CB THR C 21 " ideal model delta sigma weight residual 116.63 112.22 4.41 1.16e+00 7.43e-01 1.45e+01 angle pdb=" C THR B 21 " pdb=" CA THR B 21 " pdb=" CB THR B 21 " ideal model delta sigma weight residual 116.63 112.24 4.39 1.16e+00 7.43e-01 1.43e+01 angle pdb=" CA THR D 19 " pdb=" CB THR D 19 " pdb=" OG1 THR D 19 " ideal model delta sigma weight residual 109.60 104.55 5.05 1.50e+00 4.44e-01 1.13e+01 ... (remaining 41043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 16845 17.25 - 34.49: 699 34.49 - 51.74: 124 51.74 - 68.99: 36 68.99 - 86.24: 12 Dihedral angle restraints: 17716 sinusoidal: 6640 harmonic: 11076 Sorted by residual: dihedral pdb=" CB GLU B 608 " pdb=" CG GLU B 608 " pdb=" CD GLU B 608 " pdb=" OE1 GLU B 608 " ideal model delta sinusoidal sigma weight residual 0.00 -86.24 86.24 1 3.00e+01 1.11e-03 9.97e+00 dihedral pdb=" CB GLU D 608 " pdb=" CG GLU D 608 " pdb=" CD GLU D 608 " pdb=" OE1 GLU D 608 " ideal model delta sinusoidal sigma weight residual 0.00 -86.21 86.21 1 3.00e+01 1.11e-03 9.96e+00 dihedral pdb=" CB GLU A 608 " pdb=" CG GLU A 608 " pdb=" CD GLU A 608 " pdb=" OE1 GLU A 608 " ideal model delta sinusoidal sigma weight residual 0.00 -86.20 86.20 1 3.00e+01 1.11e-03 9.96e+00 ... (remaining 17713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 3178 0.028 - 0.057: 1065 0.057 - 0.085: 311 0.085 - 0.113: 141 0.113 - 0.141: 25 Chirality restraints: 4720 Sorted by residual: chirality pdb=" CA ILE A 271 " pdb=" N ILE A 271 " pdb=" C ILE A 271 " pdb=" CB ILE A 271 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ILE D 271 " pdb=" N ILE D 271 " pdb=" C ILE D 271 " pdb=" CB ILE D 271 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ILE C 271 " pdb=" N ILE C 271 " pdb=" C ILE C 271 " pdb=" CB ILE C 271 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.87e-01 ... (remaining 4717 not shown) Planarity restraints: 5176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D1076 " 0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO D1077 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO D1077 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D1077 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C1076 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO C1077 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO C1077 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C1077 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A1076 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO A1077 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A1077 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A1077 " 0.020 5.00e-02 4.00e+02 ... (remaining 5173 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 3233 2.74 - 3.28: 31194 3.28 - 3.82: 50332 3.82 - 4.36: 56807 4.36 - 4.90: 100827 Nonbonded interactions: 242393 Sorted by model distance: nonbonded pdb=" OE2 GLU A 828 " pdb="CA CA A2001 " model vdw 2.194 2.510 nonbonded pdb=" OE2 GLU B 828 " pdb="CA CA B2001 " model vdw 2.194 2.510 nonbonded pdb=" OE2 GLU D 828 " pdb="CA CA D2001 " model vdw 2.195 2.510 nonbonded pdb=" OE2 GLU C 828 " pdb="CA CA C2001 " model vdw 2.195 2.510 nonbonded pdb=" OE1 GLN C 831 " pdb="CA CA C2001 " model vdw 2.235 2.510 ... (remaining 242388 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' 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: 4.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 31.410 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 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 : 0.004 0.035 30188 Z= 0.218 Angle : 0.493 5.997 41048 Z= 0.287 Chirality : 0.034 0.141 4720 Planarity : 0.003 0.036 5176 Dihedral : 10.724 86.236 10548 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.82 % Allowed : 4.25 % Favored : 94.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.22 (0.15), residues: 3776 helix: 2.66 (0.11), residues: 2376 sheet: -1.28 (0.32), residues: 284 loop : -0.41 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1064 TYR 0.007 0.001 TYR C 968 PHE 0.010 0.001 PHE C 627 TRP 0.010 0.001 TRP C1124 HIS 0.004 0.001 HIS C1128 Details of bonding type rmsd covalent geometry : bond 0.00437 (30188) covalent geometry : angle 0.49337 (41048) hydrogen bonds : bond 0.12293 ( 1830) hydrogen bonds : angle 5.03469 ( 5298) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 509 MET cc_start: 0.8644 (tmm) cc_final: 0.8422 (tmm) outliers start: 24 outliers final: 6 residues processed: 127 average time/residue: 0.2084 time to fit residues: 43.2452 Evaluate side-chains 97 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain D residue 603 GLU Chi-restraints excluded: chain D residue 709 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 40.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 973 GLN B 973 GLN C 973 GLN D 295 GLN D 973 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.053538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.038633 restraints weight = 161374.789| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 3.27 r_work: 0.2778 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 30188 Z= 0.211 Angle : 0.541 6.643 41048 Z= 0.275 Chirality : 0.037 0.137 4720 Planarity : 0.004 0.049 5176 Dihedral : 4.110 61.530 4178 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.65 % Allowed : 5.59 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.14), residues: 3776 helix: 2.60 (0.11), residues: 2392 sheet: -1.08 (0.34), residues: 256 loop : -0.51 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 459 TYR 0.009 0.001 TYR D 211 PHE 0.012 0.001 PHE B1069 TRP 0.013 0.001 TRP A1124 HIS 0.006 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00490 (30188) covalent geometry : angle 0.54145 (41048) hydrogen bonds : bond 0.04422 ( 1830) hydrogen bonds : angle 4.28487 ( 5298) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 1.196 Fit side-chains REVERT: A 603 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7586 (tt0) REVERT: A 637 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8311 (ptp-170) REVERT: B 599 MET cc_start: 0.9108 (mtp) cc_final: 0.8554 (mtp) REVERT: C 284 MET cc_start: 0.8583 (mmt) cc_final: 0.8259 (mmt) outliers start: 19 outliers final: 4 residues processed: 98 average time/residue: 0.2034 time to fit residues: 33.4825 Evaluate side-chains 94 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain D residue 709 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 143 optimal weight: 7.9990 chunk 138 optimal weight: 0.0670 chunk 265 optimal weight: 3.9990 chunk 315 optimal weight: 20.0000 chunk 220 optimal weight: 20.0000 chunk 164 optimal weight: 9.9990 chunk 197 optimal weight: 20.0000 chunk 23 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 21 optimal weight: 20.0000 overall best weight: 3.5924 ------------------------------------------------------------------------------- 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 = 0.3498 r_free = 0.3498 target = 0.053873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.038920 restraints weight = 160125.079| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 3.34 r_work: 0.2782 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 30188 Z= 0.169 Angle : 0.487 6.532 41048 Z= 0.249 Chirality : 0.036 0.134 4720 Planarity : 0.004 0.051 5176 Dihedral : 3.884 54.365 4175 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.96 % Allowed : 6.34 % Favored : 92.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.14), residues: 3776 helix: 2.60 (0.11), residues: 2392 sheet: -1.37 (0.32), residues: 284 loop : -0.39 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 437 TYR 0.007 0.001 TYR D 211 PHE 0.012 0.001 PHE C 627 TRP 0.013 0.001 TRP A1124 HIS 0.004 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00388 (30188) covalent geometry : angle 0.48715 (41048) hydrogen bonds : bond 0.03880 ( 1830) hydrogen bonds : angle 4.08162 ( 5298) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 1.242 Fit side-chains REVERT: A 284 MET cc_start: 0.8952 (mmt) cc_final: 0.8469 (mmt) REVERT: A 637 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8295 (ptp-170) REVERT: B 599 MET cc_start: 0.9111 (mtp) cc_final: 0.8796 (mtp) REVERT: C 355 MET cc_start: 0.8812 (mmm) cc_final: 0.8569 (mmm) REVERT: D 284 MET cc_start: 0.8978 (mmt) cc_final: 0.8686 (mmt) REVERT: D 603 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7500 (tt0) outliers start: 28 outliers final: 14 residues processed: 106 average time/residue: 0.1866 time to fit residues: 33.8817 Evaluate side-chains 102 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 603 GLU Chi-restraints excluded: chain D residue 637 ARG Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 709 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 54 optimal weight: 0.7980 chunk 163 optimal weight: 4.9990 chunk 208 optimal weight: 30.0000 chunk 279 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 142 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 37 optimal weight: 8.9990 chunk 195 optimal weight: 5.9990 chunk 330 optimal weight: 1.9990 chunk 326 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.054394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.039468 restraints weight = 158980.289| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.31 r_work: 0.2803 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 30188 Z= 0.113 Angle : 0.452 6.790 41048 Z= 0.229 Chirality : 0.035 0.133 4720 Planarity : 0.004 0.050 5176 Dihedral : 3.618 21.103 4172 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.07 % Favored : 96.85 % Rotamer: Outliers : 1.06 % Allowed : 7.17 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.14), residues: 3776 helix: 2.69 (0.11), residues: 2392 sheet: -1.33 (0.32), residues: 284 loop : -0.42 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 459 TYR 0.006 0.001 TYR A 211 PHE 0.011 0.001 PHE D 899 TRP 0.012 0.001 TRP B1124 HIS 0.003 0.000 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00250 (30188) covalent geometry : angle 0.45202 (41048) hydrogen bonds : bond 0.03444 ( 1830) hydrogen bonds : angle 3.91331 ( 5298) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 1.229 Fit side-chains REVERT: A 284 MET cc_start: 0.8942 (mmt) cc_final: 0.8704 (mmt) REVERT: B 599 MET cc_start: 0.9091 (mtp) cc_final: 0.8805 (mtp) REVERT: C 355 MET cc_start: 0.8853 (mmm) cc_final: 0.8574 (mmm) REVERT: D 284 MET cc_start: 0.8964 (mmt) cc_final: 0.8722 (mmt) REVERT: D 603 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7464 (tt0) outliers start: 31 outliers final: 19 residues processed: 107 average time/residue: 0.1874 time to fit residues: 34.9235 Evaluate side-chains 106 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 927 MET Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 603 GLU Chi-restraints excluded: chain D residue 637 ARG Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 900 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 322 optimal weight: 2.9990 chunk 208 optimal weight: 20.0000 chunk 278 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 chunk 340 optimal weight: 5.9990 chunk 249 optimal weight: 5.9990 chunk 1 optimal weight: 50.0000 chunk 175 optimal weight: 0.5980 chunk 233 optimal weight: 0.9990 chunk 111 optimal weight: 20.0000 chunk 299 optimal weight: 0.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.054309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.039432 restraints weight = 159710.458| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.31 r_work: 0.2804 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 30188 Z= 0.124 Angle : 0.449 6.758 41048 Z= 0.227 Chirality : 0.035 0.132 4720 Planarity : 0.004 0.051 5176 Dihedral : 3.557 20.770 4172 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.97 % Favored : 96.93 % Rotamer: Outliers : 1.13 % Allowed : 7.65 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.32 (0.14), residues: 3776 helix: 2.74 (0.11), residues: 2392 sheet: -1.28 (0.32), residues: 284 loop : -0.41 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 459 TYR 0.006 0.001 TYR B 464 PHE 0.012 0.001 PHE C 627 TRP 0.012 0.001 TRP B1124 HIS 0.003 0.000 HIS D1128 Details of bonding type rmsd covalent geometry : bond 0.00281 (30188) covalent geometry : angle 0.44895 (41048) hydrogen bonds : bond 0.03397 ( 1830) hydrogen bonds : angle 3.84845 ( 5298) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 84 time to evaluate : 1.244 Fit side-chains REVERT: A 284 MET cc_start: 0.8935 (mmt) cc_final: 0.8720 (mmt) REVERT: A 637 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8350 (ptp-170) REVERT: B 355 MET cc_start: 0.8745 (mmm) cc_final: 0.8542 (mmm) REVERT: B 599 MET cc_start: 0.9085 (mtp) cc_final: 0.8817 (mtp) REVERT: C 355 MET cc_start: 0.8857 (mmm) cc_final: 0.8577 (mmm) REVERT: D 284 MET cc_start: 0.8938 (mmt) cc_final: 0.8719 (mmt) REVERT: D 603 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7440 (tt0) outliers start: 33 outliers final: 27 residues processed: 105 average time/residue: 0.1810 time to fit residues: 33.2443 Evaluate side-chains 113 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 927 MET Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 927 MET Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 603 GLU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 637 ARG Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 927 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 176 optimal weight: 10.0000 chunk 227 optimal weight: 9.9990 chunk 370 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 371 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 277 optimal weight: 10.0000 chunk 329 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 320 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.054097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.039429 restraints weight = 161843.136| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.27 r_work: 0.2796 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 30188 Z= 0.151 Angle : 0.459 7.128 41048 Z= 0.231 Chirality : 0.035 0.131 4720 Planarity : 0.004 0.052 5176 Dihedral : 3.539 21.287 4172 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.02 % Favored : 96.88 % Rotamer: Outliers : 1.23 % Allowed : 8.33 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.15), residues: 3776 helix: 2.75 (0.11), residues: 2392 sheet: -1.22 (0.32), residues: 284 loop : -0.41 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D1147 TYR 0.007 0.001 TYR C 464 PHE 0.013 0.001 PHE C 627 TRP 0.013 0.001 TRP A1124 HIS 0.004 0.001 HIS D1128 Details of bonding type rmsd covalent geometry : bond 0.00346 (30188) covalent geometry : angle 0.45868 (41048) hydrogen bonds : bond 0.03498 ( 1830) hydrogen bonds : angle 3.83963 ( 5298) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 84 time to evaluate : 1.186 Fit side-chains REVERT: A 284 MET cc_start: 0.8915 (mmt) cc_final: 0.8715 (mmt) REVERT: A 637 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8281 (ptp-170) REVERT: B 355 MET cc_start: 0.8846 (mmm) cc_final: 0.8604 (mmm) REVERT: B 599 MET cc_start: 0.9115 (mtp) cc_final: 0.8870 (mtp) REVERT: C 509 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.9007 (ptp) REVERT: D 603 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7549 (tt0) outliers start: 36 outliers final: 26 residues processed: 109 average time/residue: 0.1810 time to fit residues: 34.6441 Evaluate side-chains 113 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 927 MET Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 927 MET Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 603 GLU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 637 ARG Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 927 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 153 optimal weight: 2.9990 chunk 375 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 chunk 332 optimal weight: 0.9980 chunk 133 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 64 optimal weight: 0.0020 chunk 17 optimal weight: 9.9990 chunk 219 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1014 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.054772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.040307 restraints weight = 160517.868| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.24 r_work: 0.2831 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 30188 Z= 0.094 Angle : 0.430 7.674 41048 Z= 0.217 Chirality : 0.034 0.134 4720 Planarity : 0.004 0.050 5176 Dihedral : 3.485 19.644 4172 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.99 % Favored : 96.90 % Rotamer: Outliers : 1.03 % Allowed : 8.71 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.15), residues: 3776 helix: 2.75 (0.11), residues: 2404 sheet: -1.62 (0.33), residues: 264 loop : -0.32 (0.20), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 437 TYR 0.005 0.001 TYR D 464 PHE 0.012 0.001 PHE C 899 TRP 0.012 0.001 TRP B1124 HIS 0.002 0.000 HIS D1128 Details of bonding type rmsd covalent geometry : bond 0.00201 (30188) covalent geometry : angle 0.42979 (41048) hydrogen bonds : bond 0.03133 ( 1830) hydrogen bonds : angle 3.72244 ( 5298) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 1.250 Fit side-chains REVERT: A 637 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8467 (ptp-170) REVERT: B 355 MET cc_start: 0.8851 (mmm) cc_final: 0.8602 (mmm) REVERT: B 599 MET cc_start: 0.9095 (mtp) cc_final: 0.8883 (mtp) REVERT: C 509 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8960 (ptp) REVERT: D 430 MET cc_start: 0.9211 (mmt) cc_final: 0.8937 (mmm) REVERT: D 603 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7433 (tt0) outliers start: 30 outliers final: 19 residues processed: 106 average time/residue: 0.1773 time to fit residues: 32.9709 Evaluate side-chains 106 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 927 MET Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 927 MET Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 603 GLU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 637 ARG Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 927 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 216 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 151 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 chunk 350 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 373 optimal weight: 0.0170 chunk 129 optimal weight: 8.9990 chunk 381 optimal weight: 0.8980 overall best weight: 0.7622 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.054841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.040268 restraints weight = 159739.591| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.20 r_work: 0.2851 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 30188 Z= 0.087 Angle : 0.423 7.997 41048 Z= 0.213 Chirality : 0.034 0.135 4720 Planarity : 0.004 0.050 5176 Dihedral : 3.406 19.108 4172 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.60 % Favored : 97.30 % Rotamer: Outliers : 1.03 % Allowed : 8.85 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.15), residues: 3776 helix: 2.78 (0.11), residues: 2408 sheet: -1.15 (0.32), residues: 284 loop : -0.31 (0.20), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 437 TYR 0.005 0.001 TYR D 464 PHE 0.013 0.001 PHE C 899 TRP 0.012 0.001 TRP A 579 HIS 0.002 0.000 HIS D1128 Details of bonding type rmsd covalent geometry : bond 0.00178 (30188) covalent geometry : angle 0.42269 (41048) hydrogen bonds : bond 0.02979 ( 1830) hydrogen bonds : angle 3.64216 ( 5298) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 1.244 Fit side-chains REVERT: A 637 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8455 (ptp-170) REVERT: B 355 MET cc_start: 0.8835 (mmm) cc_final: 0.8586 (mmm) REVERT: B 599 MET cc_start: 0.9074 (mtp) cc_final: 0.8854 (mtp) REVERT: C 509 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8969 (ptp) REVERT: D 603 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7342 (tt0) outliers start: 30 outliers final: 22 residues processed: 105 average time/residue: 0.1847 time to fit residues: 33.7247 Evaluate side-chains 109 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 927 MET Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 927 MET Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 603 GLU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 637 ARG Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 709 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 82 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 204 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 354 optimal weight: 9.9990 chunk 324 optimal weight: 8.9990 chunk 272 optimal weight: 2.9990 chunk 205 optimal weight: 10.0000 chunk 277 optimal weight: 9.9990 chunk 170 optimal weight: 0.5980 chunk 268 optimal weight: 0.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.053901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.038869 restraints weight = 160425.454| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 3.33 r_work: 0.2782 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30188 Z= 0.184 Angle : 0.491 9.954 41048 Z= 0.244 Chirality : 0.036 0.127 4720 Planarity : 0.004 0.052 5176 Dihedral : 3.477 22.886 4172 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.89 % Favored : 97.01 % Rotamer: Outliers : 1.03 % Allowed : 8.95 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.43 (0.15), residues: 3776 helix: 2.77 (0.11), residues: 2408 sheet: -1.12 (0.32), residues: 284 loop : -0.33 (0.20), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 601 TYR 0.008 0.001 TYR B 464 PHE 0.014 0.001 PHE C 627 TRP 0.017 0.001 TRP A 579 HIS 0.004 0.001 HIS D1128 Details of bonding type rmsd covalent geometry : bond 0.00421 (30188) covalent geometry : angle 0.49058 (41048) hydrogen bonds : bond 0.03587 ( 1830) hydrogen bonds : angle 3.80302 ( 5298) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 1.250 Fit side-chains REVERT: A 637 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8288 (ptp-170) REVERT: B 355 MET cc_start: 0.8829 (mmm) cc_final: 0.8576 (mmm) REVERT: B 599 MET cc_start: 0.9088 (mtp) cc_final: 0.8843 (mtp) REVERT: C 509 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.8993 (ptp) REVERT: D 603 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7493 (tt0) outliers start: 30 outliers final: 22 residues processed: 107 average time/residue: 0.1811 time to fit residues: 33.5854 Evaluate side-chains 109 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 927 MET Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 927 MET Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 603 GLU Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 709 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 96 optimal weight: 20.0000 chunk 285 optimal weight: 7.9990 chunk 271 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 288 optimal weight: 20.0000 chunk 135 optimal weight: 4.9990 chunk 123 optimal weight: 30.0000 chunk 332 optimal weight: 8.9990 chunk 351 optimal weight: 0.9980 chunk 266 optimal weight: 0.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.054086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.039456 restraints weight = 161688.142| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.22 r_work: 0.2800 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 30188 Z= 0.154 Angle : 0.470 11.464 41048 Z= 0.234 Chirality : 0.035 0.130 4720 Planarity : 0.004 0.052 5176 Dihedral : 3.505 23.365 4172 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.86 % Favored : 97.03 % Rotamer: Outliers : 0.89 % Allowed : 9.09 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.42 (0.15), residues: 3776 helix: 2.76 (0.11), residues: 2408 sheet: -1.11 (0.32), residues: 284 loop : -0.33 (0.20), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1147 TYR 0.006 0.001 TYR B 464 PHE 0.012 0.001 PHE C 627 TRP 0.013 0.001 TRP B1124 HIS 0.004 0.001 HIS D1128 Details of bonding type rmsd covalent geometry : bond 0.00354 (30188) covalent geometry : angle 0.46955 (41048) hydrogen bonds : bond 0.03455 ( 1830) hydrogen bonds : angle 3.78766 ( 5298) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 1.283 Fit side-chains REVERT: A 637 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8262 (ptp-170) REVERT: B 355 MET cc_start: 0.8872 (mmm) cc_final: 0.8612 (mmm) REVERT: B 599 MET cc_start: 0.9086 (mtp) cc_final: 0.8874 (mtp) REVERT: C 509 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.9003 (ptp) outliers start: 26 outliers final: 21 residues processed: 103 average time/residue: 0.1818 time to fit residues: 32.9258 Evaluate side-chains 107 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 927 MET Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 636 VAL Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 927 MET Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 709 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 301 optimal weight: 7.9990 chunk 123 optimal weight: 30.0000 chunk 127 optimal weight: 0.1980 chunk 356 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 63 optimal weight: 0.8980 chunk 198 optimal weight: 7.9990 chunk 290 optimal weight: 7.9990 chunk 236 optimal weight: 4.9990 chunk 331 optimal weight: 0.0570 overall best weight: 1.8302 ------------------------------------------------------------------------------- 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 = 0.3516 r_free = 0.3516 target = 0.054326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.039618 restraints weight = 160663.104| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 3.29 r_work: 0.2816 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 30188 Z= 0.107 Angle : 0.443 10.624 41048 Z= 0.222 Chirality : 0.034 0.133 4720 Planarity : 0.004 0.051 5176 Dihedral : 3.464 22.149 4172 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.75 % Favored : 97.14 % Rotamer: Outliers : 0.75 % Allowed : 9.19 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.43 (0.15), residues: 3776 helix: 2.76 (0.11), residues: 2408 sheet: -1.11 (0.32), residues: 284 loop : -0.29 (0.20), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 437 TYR 0.005 0.001 TYR B 464 PHE 0.011 0.001 PHE D 899 TRP 0.013 0.001 TRP B1124 HIS 0.003 0.000 HIS D1128 Details of bonding type rmsd covalent geometry : bond 0.00237 (30188) covalent geometry : angle 0.44259 (41048) hydrogen bonds : bond 0.03204 ( 1830) hydrogen bonds : angle 3.70448 ( 5298) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7174.50 seconds wall clock time: 123 minutes 51.65 seconds (7431.65 seconds total)