Starting phenix.real_space_refine on Wed Jun 25 12:49:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b94_44368/06_2025/9b94_44368.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b94_44368/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9b94_44368/06_2025/9b94_44368.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b94_44368/06_2025/9b94_44368.map" model { file = "/net/cci-nas-00/data/ceres_data/9b94_44368/06_2025/9b94_44368.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b94_44368/06_2025/9b94_44368.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 4, 'ASP:plan': 15, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 12} 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: C, B, D Time building chain proxies: 21.12, per 1000 atoms: 0.72 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: 9.27 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 3.39 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: 12.11 Time building geometry restraints manager: 10.68 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: 0.21 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.250 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 73.270 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.080 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: 0.020 Load rotamer database and sin/cos tables:3.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.930 ------------------------------------------------------------------------------- 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 : 3.94 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.001 TRP C1124 HIS 0.004 0.001 HIS C1128 PHE 0.010 0.001 PHE C 627 TYR 0.007 0.001 TYR C 968 ARG 0.002 0.000 ARG B1064 Details of bonding type rmsd hydrogen bonds : bond 0.12293 ( 1830) hydrogen bonds : angle 5.03469 ( 5298) covalent geometry : bond 0.00437 (30188) covalent geometry : angle 0.49337 (41048) *********************** 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 : 3.194 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: 0.4175 time to fit residues: 87.5816 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 : 3.171 ------------------------------------------------------------------------------- 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 324 optimal weight: 9.9990 chunk 291 optimal weight: 50.0000 chunk 161 optimal weight: 0.8980 chunk 99 optimal weight: 0.0570 chunk 196 optimal weight: 0.0070 chunk 155 optimal weight: 5.9990 chunk 300 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 chunk 224 optimal weight: 30.0000 chunk 348 optimal weight: 7.9990 overall best weight: 2.7920 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.053960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.039154 restraints weight = 159270.912| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.26 r_work: 0.2799 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30188 Z= 0.152 Angle : 0.508 6.472 41048 Z= 0.259 Chirality : 0.036 0.141 4720 Planarity : 0.004 0.047 5176 Dihedral : 4.059 61.516 4178 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.45 % Allowed : 5.42 % Favored : 94.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.15), residues: 3776 helix: 2.67 (0.11), residues: 2388 sheet: -1.38 (0.32), residues: 284 loop : -0.37 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1124 HIS 0.003 0.001 HIS D1128 PHE 0.011 0.001 PHE C 627 TYR 0.009 0.001 TYR D 211 ARG 0.005 0.000 ARG A 612 Details of bonding type rmsd hydrogen bonds : bond 0.04218 ( 1830) hydrogen bonds : angle 4.20710 ( 5298) covalent geometry : bond 0.00346 (30188) covalent geometry : angle 0.50760 (41048) *********************** 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 103 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 3.620 Fit side-chains REVERT: A 186 MET cc_start: 0.9037 (mmt) cc_final: 0.8804 (mpp) REVERT: A 603 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7508 (tt0) REVERT: D 509 MET cc_start: 0.9188 (tmm) cc_final: 0.8890 (tmm) REVERT: D 603 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7561 (tt0) outliers start: 13 outliers final: 4 residues processed: 96 average time/residue: 0.3696 time to fit residues: 62.8050 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 : 3.118 ------------------------------------------------------------------------------- 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 242 optimal weight: 1.9990 chunk 337 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 chunk 362 optimal weight: 0.9980 chunk 247 optimal weight: 0.9990 chunk 10 optimal weight: 0.0470 chunk 186 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 114 optimal weight: 30.0000 chunk 224 optimal weight: 8.9990 chunk 253 optimal weight: 7.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.054676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.039797 restraints weight = 159100.537| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.34 r_work: 0.2816 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1243 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= 0.106 Angle : 0.453 6.740 41048 Z= 0.231 Chirality : 0.035 0.134 4720 Planarity : 0.004 0.049 5176 Dihedral : 3.930 54.017 4178 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.72 % Allowed : 6.34 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.14), residues: 3776 helix: 2.73 (0.11), residues: 2388 sheet: -1.37 (0.32), residues: 284 loop : -0.38 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1124 HIS 0.002 0.001 HIS D1128 PHE 0.012 0.001 PHE D 899 TYR 0.006 0.001 TYR D 211 ARG 0.009 0.000 ARG B 459 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 1830) hydrogen bonds : angle 3.94787 ( 5298) covalent geometry : bond 0.00226 (30188) covalent geometry : angle 0.45289 (41048) *********************** 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 109 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 4.196 Fit side-chains REVERT: A 637 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8506 (ptp-170) REVERT: C 355 MET cc_start: 0.8770 (mmm) cc_final: 0.8491 (mmm) REVERT: D 284 MET cc_start: 0.8969 (mmt) cc_final: 0.8682 (mmt) REVERT: D 509 MET cc_start: 0.9212 (tmm) cc_final: 0.8945 (tmm) outliers start: 21 outliers final: 8 residues processed: 100 average time/residue: 0.5531 time to fit residues: 99.0861 Evaluate side-chains 97 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 4.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 637 ARG 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 136 optimal weight: 9.9990 chunk 338 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 195 optimal weight: 0.0020 chunk 187 optimal weight: 10.0000 chunk 18 optimal weight: 30.0000 chunk 168 optimal weight: 0.7980 chunk 270 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 269 optimal weight: 6.9990 overall best weight: 2.3392 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.054500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.039604 restraints weight = 160633.261| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.32 r_work: 0.2809 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 30188 Z= 0.125 Angle : 0.452 6.991 41048 Z= 0.228 Chirality : 0.035 0.131 4720 Planarity : 0.004 0.050 5176 Dihedral : 3.542 19.832 4172 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.94 % Favored : 96.95 % Rotamer: Outliers : 0.89 % Allowed : 6.82 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.14), residues: 3776 helix: 2.75 (0.11), residues: 2392 sheet: -1.32 (0.32), residues: 284 loop : -0.41 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1124 HIS 0.003 0.001 HIS D1128 PHE 0.012 0.001 PHE C 627 TYR 0.006 0.001 TYR A 464 ARG 0.010 0.000 ARG D 459 Details of bonding type rmsd hydrogen bonds : bond 0.03435 ( 1830) hydrogen bonds : angle 3.87040 ( 5298) covalent geometry : bond 0.00281 (30188) covalent geometry : angle 0.45208 (41048) *********************** 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 114 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 3.765 Fit side-chains REVERT: A 186 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8654 (mpp) REVERT: A 637 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8503 (ptp-170) REVERT: B 355 MET cc_start: 0.8729 (mmm) cc_final: 0.8481 (mmm) REVERT: B 509 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.9012 (tmm) REVERT: C 355 MET cc_start: 0.8826 (mmm) cc_final: 0.8557 (mmm) REVERT: D 284 MET cc_start: 0.8967 (mmt) cc_final: 0.8727 (mmt) REVERT: D 509 MET cc_start: 0.9242 (tmm) cc_final: 0.9007 (tmm) outliers start: 26 outliers final: 17 residues processed: 102 average time/residue: 0.3800 time to fit residues: 67.7030 Evaluate side-chains 108 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 3.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 900 MET 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 509 MET 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 509 MET Chi-restraints excluded: chain C residue 637 ARG 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 637 ARG Chi-restraints excluded: chain D residue 709 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 278 optimal weight: 5.9990 chunk 334 optimal weight: 5.9990 chunk 250 optimal weight: 7.9990 chunk 347 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 352 optimal weight: 0.4980 chunk 327 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 264 optimal weight: 1.9990 chunk 275 optimal weight: 9.9990 chunk 345 optimal weight: 1.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.054630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.039761 restraints weight = 159463.248| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 3.31 r_work: 0.2815 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 30188 Z= 0.115 Angle : 0.438 7.134 41048 Z= 0.222 Chirality : 0.034 0.133 4720 Planarity : 0.004 0.050 5176 Dihedral : 3.490 19.334 4172 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.78 % Favored : 97.11 % Rotamer: Outliers : 1.37 % Allowed : 7.24 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.14), residues: 3776 helix: 2.79 (0.11), residues: 2392 sheet: -1.25 (0.32), residues: 284 loop : -0.41 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1124 HIS 0.003 0.000 HIS D1128 PHE 0.012 0.001 PHE C 627 TYR 0.006 0.001 TYR C 464 ARG 0.002 0.000 ARG B 437 Details of bonding type rmsd hydrogen bonds : bond 0.03298 ( 1830) hydrogen bonds : angle 3.79080 ( 5298) covalent geometry : bond 0.00257 (30188) covalent geometry : angle 0.43758 (41048) *********************** 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 126 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 86 time to evaluate : 3.272 Fit side-chains REVERT: A 186 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8672 (mpp) REVERT: A 637 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8492 (ptp-170) REVERT: B 355 MET cc_start: 0.8800 (mmm) cc_final: 0.8546 (mmm) REVERT: B 509 MET cc_start: 0.9334 (OUTLIER) cc_final: 0.8973 (tmm) REVERT: C 355 MET cc_start: 0.8831 (mmm) cc_final: 0.8560 (mmm) REVERT: D 284 MET cc_start: 0.8930 (mmt) cc_final: 0.8714 (mmt) REVERT: D 509 MET cc_start: 0.9248 (tmm) cc_final: 0.9018 (tmm) outliers start: 40 outliers final: 23 residues processed: 107 average time/residue: 0.3869 time to fit residues: 71.8461 Evaluate side-chains 112 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 3.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 186 MET 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 900 MET Chi-restraints excluded: chain A residue 927 MET Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 637 ARG 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 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 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 38 optimal weight: 10.0000 chunk 125 optimal weight: 30.0000 chunk 97 optimal weight: 50.0000 chunk 212 optimal weight: 6.9990 chunk 148 optimal weight: 6.9990 chunk 326 optimal weight: 9.9990 chunk 237 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 367 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 378 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.053432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.038508 restraints weight = 162056.083| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.31 r_work: 0.2772 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 30188 Z= 0.217 Angle : 0.510 7.097 41048 Z= 0.255 Chirality : 0.036 0.128 4720 Planarity : 0.004 0.053 5176 Dihedral : 3.603 23.071 4172 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.10 % Favored : 96.80 % Rotamer: Outliers : 1.20 % Allowed : 7.96 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.14), residues: 3776 helix: 2.70 (0.11), residues: 2400 sheet: -1.16 (0.32), residues: 280 loop : -0.41 (0.20), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1124 HIS 0.005 0.001 HIS D1128 PHE 0.015 0.001 PHE C 627 TYR 0.008 0.001 TYR B 464 ARG 0.002 0.000 ARG B 601 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 1830) hydrogen bonds : angle 3.94149 ( 5298) covalent geometry : bond 0.00497 (30188) covalent geometry : angle 0.50998 (41048) *********************** 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 119 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 84 time to evaluate : 3.200 Fit side-chains REVERT: A 186 MET cc_start: 0.9083 (mpp) cc_final: 0.8774 (mpp) REVERT: A 637 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8365 (ptp-170) REVERT: B 509 MET cc_start: 0.9313 (OUTLIER) cc_final: 0.8966 (tmm) REVERT: C 509 MET cc_start: 0.9256 (OUTLIER) cc_final: 0.9043 (ptp) REVERT: D 284 MET cc_start: 0.8921 (mmt) cc_final: 0.8712 (mmt) REVERT: D 509 MET cc_start: 0.9280 (tmm) cc_final: 0.9041 (tmm) outliers start: 35 outliers final: 25 residues processed: 106 average time/residue: 0.3901 time to fit residues: 72.8306 Evaluate side-chains 112 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 3.513 ------------------------------------------------------------------------------- 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 622 MET 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 509 MET Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 636 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 509 MET Chi-restraints excluded: chain C residue 622 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 378 LEU Chi-restraints excluded: chain D residue 574 MET Chi-restraints excluded: chain D residue 622 MET Chi-restraints excluded: chain D residue 636 VAL 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 112 optimal weight: 20.0000 chunk 148 optimal weight: 4.9990 chunk 246 optimal weight: 0.4980 chunk 5 optimal weight: 20.0000 chunk 365 optimal weight: 4.9990 chunk 326 optimal weight: 8.9990 chunk 167 optimal weight: 0.9990 chunk 105 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 chunk 313 optimal weight: 4.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1014 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.054223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.039596 restraints weight = 161871.856| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.24 r_work: 0.2803 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 30188 Z= 0.133 Angle : 0.452 7.642 41048 Z= 0.229 Chirality : 0.035 0.131 4720 Planarity : 0.004 0.052 5176 Dihedral : 3.571 21.736 4172 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.97 % Favored : 96.93 % Rotamer: Outliers : 1.13 % Allowed : 8.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.14), residues: 3776 helix: 2.76 (0.11), residues: 2392 sheet: -1.26 (0.32), residues: 284 loop : -0.40 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1124 HIS 0.003 0.000 HIS D1128 PHE 0.011 0.001 PHE C 627 TYR 0.006 0.001 TYR C 464 ARG 0.002 0.000 ARG A1147 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 1830) hydrogen bonds : angle 3.83174 ( 5298) covalent geometry : bond 0.00302 (30188) covalent geometry : angle 0.45181 (41048) *********************** 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 117 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 84 time to evaluate : 3.605 Fit side-chains REVERT: A 186 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8746 (mmt) REVERT: A 637 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8409 (ptp-170) REVERT: B 509 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.8943 (tmm) REVERT: C 355 MET cc_start: 0.8762 (mmm) cc_final: 0.8416 (mmm) REVERT: C 509 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.9002 (ptp) REVERT: D 430 MET cc_start: 0.9293 (mmt) cc_final: 0.8920 (mmm) REVERT: D 509 MET cc_start: 0.9260 (tmm) cc_final: 0.9040 (tmm) outliers start: 33 outliers final: 22 residues processed: 105 average time/residue: 0.4095 time to fit residues: 78.0442 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 : 3.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 MET 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 506 VAL Chi-restraints excluded: chain B residue 509 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 509 MET Chi-restraints excluded: chain C residue 622 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 574 MET Chi-restraints excluded: chain D residue 622 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 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 99 optimal weight: 0.0370 chunk 151 optimal weight: 0.0980 chunk 70 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 293 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 280 optimal weight: 8.9990 chunk 317 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 357 optimal weight: 0.9980 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1014 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.054913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.040439 restraints weight = 161703.239| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.23 r_work: 0.2838 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 30188 Z= 0.091 Angle : 0.427 7.158 41048 Z= 0.217 Chirality : 0.034 0.135 4720 Planarity : 0.004 0.051 5176 Dihedral : 3.478 19.769 4172 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.75 % Favored : 97.14 % Rotamer: Outliers : 0.99 % Allowed : 8.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.15), residues: 3776 helix: 2.76 (0.11), residues: 2408 sheet: -1.20 (0.32), residues: 284 loop : -0.31 (0.20), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 579 HIS 0.002 0.000 HIS D1128 PHE 0.013 0.001 PHE C 899 TYR 0.005 0.001 TYR C 464 ARG 0.002 0.000 ARG A 459 Details of bonding type rmsd hydrogen bonds : bond 0.03100 ( 1830) hydrogen bonds : angle 3.69910 ( 5298) covalent geometry : bond 0.00190 (30188) covalent geometry : angle 0.42740 (41048) *********************** 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: 29 poor density : 85 time to evaluate : 3.354 Fit side-chains REVERT: A 186 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8686 (mpp) REVERT: A 603 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7468 (tt0) REVERT: A 637 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8577 (ptp-170) REVERT: B 509 MET cc_start: 0.9308 (OUTLIER) cc_final: 0.8944 (tmm) REVERT: C 355 MET cc_start: 0.8761 (mmm) cc_final: 0.8421 (mmm) REVERT: C 509 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8978 (ptp) REVERT: D 186 MET cc_start: 0.9114 (mmm) cc_final: 0.8844 (mpp) REVERT: D 509 MET cc_start: 0.9261 (tmm) cc_final: 0.9049 (tmm) outliers start: 29 outliers final: 22 residues processed: 104 average time/residue: 0.4080 time to fit residues: 74.6844 Evaluate side-chains 111 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 3.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 603 GLU 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 509 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 927 MET Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 622 MET 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 927 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 Chi-restraints excluded: chain D residue 927 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 67 optimal weight: 0.1980 chunk 127 optimal weight: 20.0000 chunk 99 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 358 optimal weight: 8.9990 chunk 316 optimal weight: 50.0000 chunk 48 optimal weight: 5.9990 chunk 327 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 191 optimal weight: 2.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.054234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.039474 restraints weight = 159968.280| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.26 r_work: 0.2812 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30188 Z= 0.131 Angle : 0.450 12.805 41048 Z= 0.225 Chirality : 0.035 0.130 4720 Planarity : 0.004 0.052 5176 Dihedral : 3.442 20.712 4172 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.62 % Favored : 97.27 % Rotamer: Outliers : 1.10 % Allowed : 9.05 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.14), residues: 3776 helix: 2.78 (0.11), residues: 2404 sheet: -1.16 (0.32), residues: 284 loop : -0.32 (0.20), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 579 HIS 0.003 0.000 HIS D1128 PHE 0.013 0.001 PHE A 627 TYR 0.007 0.001 TYR C 464 ARG 0.002 0.000 ARG B 612 Details of bonding type rmsd hydrogen bonds : bond 0.03285 ( 1830) hydrogen bonds : angle 3.72761 ( 5298) covalent geometry : bond 0.00299 (30188) covalent geometry : angle 0.44982 (41048) *********************** 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 116 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 84 time to evaluate : 3.346 Fit side-chains REVERT: A 637 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8505 (ptp-170) REVERT: B 509 MET cc_start: 0.9283 (OUTLIER) cc_final: 0.8924 (tmm) REVERT: C 355 MET cc_start: 0.8787 (mmm) cc_final: 0.8438 (mmm) REVERT: C 509 MET cc_start: 0.9212 (OUTLIER) cc_final: 0.8994 (ptp) REVERT: D 186 MET cc_start: 0.9115 (mmm) cc_final: 0.8736 (mpp) REVERT: D 509 MET cc_start: 0.9260 (tmm) cc_final: 0.9052 (tmm) outliers start: 32 outliers final: 26 residues processed: 107 average time/residue: 0.3746 time to fit residues: 70.4445 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 : 3.106 ------------------------------------------------------------------------------- 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 509 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 927 MET Chi-restraints excluded: chain B residue 1162 LEU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 622 MET 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 927 MET Chi-restraints excluded: chain D residue 137 LEU 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 Chi-restraints excluded: chain D residue 927 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 282 optimal weight: 6.9990 chunk 237 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 140 optimal weight: 0.4980 chunk 164 optimal weight: 7.9990 chunk 87 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 231 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 330 optimal weight: 9.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.054581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.039952 restraints weight = 160156.220| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.22 r_work: 0.2834 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1811 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= 0.102 Angle : 0.435 12.520 41048 Z= 0.218 Chirality : 0.034 0.133 4720 Planarity : 0.004 0.051 5176 Dihedral : 3.411 19.759 4172 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.73 % Favored : 97.17 % Rotamer: Outliers : 0.93 % Allowed : 9.16 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.14), residues: 3776 helix: 2.79 (0.11), residues: 2404 sheet: -1.13 (0.32), residues: 284 loop : -0.32 (0.20), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C1124 HIS 0.003 0.000 HIS D1128 PHE 0.011 0.001 PHE D 899 TYR 0.005 0.001 TYR C 464 ARG 0.004 0.000 ARG B 611 Details of bonding type rmsd hydrogen bonds : bond 0.03117 ( 1830) hydrogen bonds : angle 3.67619 ( 5298) covalent geometry : bond 0.00225 (30188) covalent geometry : angle 0.43544 (41048) ********************** 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 111 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 3.423 Fit side-chains REVERT: A 637 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8523 (ptp-170) REVERT: B 509 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.8910 (tmm) REVERT: C 355 MET cc_start: 0.8792 (mmm) cc_final: 0.8449 (mmm) REVERT: C 509 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.9017 (ptp) REVERT: D 186 MET cc_start: 0.9098 (mmm) cc_final: 0.8695 (mpp) REVERT: D 509 MET cc_start: 0.9267 (tmm) cc_final: 0.9058 (tmm) outliers start: 27 outliers final: 24 residues processed: 103 average time/residue: 0.3713 time to fit residues: 68.0824 Evaluate side-chains 111 residues out of total 3260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 3.514 ------------------------------------------------------------------------------- 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 506 VAL Chi-restraints excluded: chain B residue 509 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 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 622 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 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 Chi-restraints excluded: chain D residue 927 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 85 optimal weight: 6.9990 chunk 162 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 366 optimal weight: 0.6980 chunk 327 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 225 optimal weight: 5.9990 chunk 306 optimal weight: 20.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 = 0.3511 r_free = 0.3511 target = 0.054177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.039383 restraints weight = 159928.333| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.30 r_work: 0.2808 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30188 Z= 0.136 Angle : 0.460 14.273 41048 Z= 0.228 Chirality : 0.035 0.130 4720 Planarity : 0.004 0.052 5176 Dihedral : 3.409 20.957 4172 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.67 % Favored : 97.22 % Rotamer: Outliers : 1.13 % Allowed : 9.05 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.14), residues: 3776 helix: 2.80 (0.11), residues: 2404 sheet: -1.13 (0.32), residues: 284 loop : -0.32 (0.20), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1124 HIS 0.003 0.001 HIS D1128 PHE 0.013 0.001 PHE A 627 TYR 0.007 0.001 TYR C 464 ARG 0.002 0.000 ARG B 612 Details of bonding type rmsd hydrogen bonds : bond 0.03315 ( 1830) hydrogen bonds : angle 3.71928 ( 5298) covalent geometry : bond 0.00309 (30188) covalent geometry : angle 0.46011 (41048) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15511.56 seconds wall clock time: 272 minutes 28.25 seconds (16348.25 seconds total)