Starting phenix.real_space_refine on Thu Jun 26 09:30:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8w_44360/06_2025/9b8w_44360.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8w_44360/06_2025/9b8w_44360.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/9b8w_44360/06_2025/9b8w_44360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8w_44360/06_2025/9b8w_44360.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8w_44360/06_2025/9b8w_44360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8w_44360/06_2025/9b8w_44360.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 8 9.91 5 S 152 5.16 5 C 19592 2.51 5 N 5344 2.21 5 O 5160 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30256 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7562 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 43, 'TRANS': 949} Chain breaks: 8 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 323 Unresolved non-hydrogen angles: 396 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 15, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 15, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 217 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, B, D Time building chain proxies: 21.09, per 1000 atoms: 0.70 Number of scatterers: 30256 At special positions: 0 Unit cell: (169.74, 168.912, 152.352, 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 8 19.99 S 152 16.00 O 5160 8.00 N 5344 7.00 C 19592 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 37 " distance=2.83 Simple disulfide: pdb=" SG CYS A 993 " - pdb=" SG CYS A1011 " distance=2.03 Simple disulfide: pdb=" SG CYS C 35 " - pdb=" SG CYS C 37 " distance=2.83 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 37 " distance=2.83 Simple disulfide: pdb=" SG CYS D 35 " - pdb=" SG CYS D 37 " distance=2.83 Simple disulfide: pdb=" SG CYS C 993 " - pdb=" SG CYS C1011 " distance=2.03 Simple disulfide: pdb=" SG CYS B 993 " - pdb=" SG CYS B1011 " distance=2.03 Simple disulfide: pdb=" SG CYS D 993 " - pdb=" SG CYS D1011 " distance=2.03 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: 8.19 Conformation dependent library (CDL) restraints added in 4.0 seconds 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7360 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 16 sheets defined 68.2% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.30 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 98 through 108 removed outlier: 3.742A pdb=" N VAL A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 150 removed outlier: 3.759A pdb=" N VAL A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 196 through 201 removed outlier: 3.588A pdb=" N THR A 199 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 200 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 201 " --> pdb=" O ASP A 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 196 through 201' Processing helix chain 'A' and resid 246 through 259 Processing helix chain 'A' and resid 264 through 268 removed outlier: 3.692A 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 318 Processing helix chain 'A' and resid 325 through 336 removed outlier: 3.589A pdb=" N GLY A 329 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 356 Processing helix chain 'A' and resid 373 through 386 removed outlier: 3.509A pdb=" N CYS A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY A 386 " --> pdb=" O VAL A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 392 No H-bonds generated for 'chain 'A' and resid 390 through 392' Processing helix chain 'A' and resid 393 through 403 Processing helix chain 'A' and resid 406 through 413 Processing helix chain 'A' and resid 421 through 435 removed outlier: 4.353A pdb=" N ALA A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.897A 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 450 through 455 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: 3.879A pdb=" N VAL A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 510 " --> pdb=" O VAL A 506 " (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 607 through 634 Processing helix chain 'A' and resid 634 through 644 removed outlier: 3.901A 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: 3.921A pdb=" N GLN A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 682 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 906 removed outlier: 3.838A pdb=" N LEU A 906 " --> pdb=" O PHE A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 912 Processing helix chain 'A' and resid 916 through 926 Processing helix chain 'A' and resid 926 through 953 Processing helix chain 'A' and resid 958 through 967 Processing helix chain 'A' and resid 967 through 975 removed outlier: 3.621A pdb=" N ILE A 974 " --> pdb=" O PRO A 970 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE A 975 " --> pdb=" O TYR A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 984 removed outlier: 3.641A pdb=" N MET A 983 " --> pdb=" O PRO A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 988 Processing helix chain 'A' and resid 1016 through 1033 removed outlier: 3.995A 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: 4.104A pdb=" N TYR A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A1071 " --> pdb=" O ARG A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1088 removed outlier: 4.103A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1142 Processing helix chain 'A' and resid 1143 through 1177 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 98 through 108 removed outlier: 3.742A pdb=" N VAL B 102 " --> pdb=" O ASP B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 150 removed outlier: 3.758A pdb=" N VAL B 143 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 176 Processing helix chain 'B' and resid 196 through 201 removed outlier: 3.588A pdb=" N THR B 199 " --> pdb=" O ASN B 196 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 200 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE B 201 " --> pdb=" O ASP B 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 196 through 201' Processing helix chain 'B' and resid 246 through 259 Processing helix chain 'B' and resid 264 through 268 removed outlier: 3.692A 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 318 Processing helix chain 'B' and resid 325 through 336 removed outlier: 3.589A pdb=" N GLY B 329 " --> pdb=" O GLY B 325 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLU B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 356 Processing helix chain 'B' and resid 373 through 386 removed outlier: 3.509A pdb=" N CYS B 385 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY B 386 " --> pdb=" O VAL B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 392 No H-bonds generated for 'chain 'B' and resid 390 through 392' Processing helix chain 'B' and resid 393 through 403 Processing helix chain 'B' and resid 406 through 413 Processing helix chain 'B' and resid 421 through 435 removed outlier: 4.353A pdb=" N ALA B 427 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 4.898A 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 450 through 455 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: 3.879A pdb=" N VAL B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 510 " --> pdb=" O VAL B 506 " (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 607 through 634 Processing helix chain 'B' and resid 634 through 644 removed outlier: 3.901A 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: 3.921A pdb=" N GLN B 669 " --> pdb=" O ALA B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 682 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 906 removed outlier: 3.839A pdb=" N LEU B 906 " --> pdb=" O PHE B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 907 through 912 Processing helix chain 'B' and resid 916 through 926 Processing helix chain 'B' and resid 926 through 953 Processing helix chain 'B' and resid 958 through 967 Processing helix chain 'B' and resid 967 through 975 removed outlier: 3.622A pdb=" N ILE B 974 " --> pdb=" O PRO B 970 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE B 975 " --> pdb=" O TYR B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 984 removed outlier: 3.640A pdb=" N MET B 983 " --> pdb=" O PRO B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 988 Processing helix chain 'B' and resid 1016 through 1033 removed outlier: 3.996A 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: 4.104A pdb=" N TYR B1063 " --> pdb=" O LYS B1059 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG B1064 " --> pdb=" O ALA B1060 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B1071 " --> pdb=" O ARG B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1079 through 1088 removed outlier: 4.103A pdb=" N SER B1083 " --> pdb=" O PHE B1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1142 Processing helix chain 'B' and resid 1143 through 1177 Processing helix chain 'C' and resid 10 through 15 Processing helix chain 'C' and resid 98 through 108 removed outlier: 3.742A pdb=" N VAL C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 150 removed outlier: 3.758A pdb=" N VAL C 143 " --> pdb=" O ARG C 139 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 196 through 201 removed outlier: 3.589A pdb=" N THR C 199 " --> pdb=" O ASN C 196 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU C 200 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE C 201 " --> pdb=" O ASP C 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 196 through 201' Processing helix chain 'C' and resid 246 through 259 Processing helix chain 'C' and resid 264 through 268 removed outlier: 3.693A 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 318 Processing helix chain 'C' and resid 325 through 336 removed outlier: 3.590A pdb=" N GLY C 329 " --> pdb=" O GLY C 325 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 356 Processing helix chain 'C' and resid 373 through 386 removed outlier: 3.509A pdb=" N CYS C 385 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY C 386 " --> pdb=" O VAL C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 392 No H-bonds generated for 'chain 'C' and resid 390 through 392' Processing helix chain 'C' and resid 393 through 403 Processing helix chain 'C' and resid 406 through 413 Processing helix chain 'C' and resid 421 through 435 removed outlier: 4.353A pdb=" N ALA C 427 " --> pdb=" O PHE C 423 " (cutoff:3.500A) removed outlier: 4.897A 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 450 through 455 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: 3.879A pdb=" N VAL C 506 " --> pdb=" O ASP C 502 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 510 " --> pdb=" O VAL C 506 " (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 607 through 634 Processing helix chain 'C' and resid 634 through 644 removed outlier: 3.901A 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: 3.921A pdb=" N GLN C 669 " --> pdb=" O ALA C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 682 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 906 removed outlier: 3.839A pdb=" N LEU C 906 " --> pdb=" O PHE C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 912 Processing helix chain 'C' and resid 916 through 926 Processing helix chain 'C' and resid 926 through 953 Processing helix chain 'C' and resid 958 through 967 Processing helix chain 'C' and resid 967 through 975 removed outlier: 3.621A pdb=" N ILE C 974 " --> pdb=" O PRO C 970 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE C 975 " --> pdb=" O TYR C 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 984 removed outlier: 3.640A pdb=" N MET C 983 " --> pdb=" O PRO C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 988 Processing helix chain 'C' and resid 1016 through 1033 removed outlier: 3.995A 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: 4.104A pdb=" N TYR C1063 " --> pdb=" O LYS C1059 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG C1064 " --> pdb=" O ALA C1060 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER C1071 " --> pdb=" O ARG C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1079 through 1088 removed outlier: 4.101A pdb=" N SER C1083 " --> pdb=" O PHE C1079 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1142 Processing helix chain 'C' and resid 1143 through 1177 Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 98 through 108 removed outlier: 3.742A pdb=" N VAL D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 150 removed outlier: 3.758A pdb=" N VAL D 143 " --> pdb=" O ARG D 139 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG D 144 " --> pdb=" O ARG D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 176 Processing helix chain 'D' and resid 196 through 201 removed outlier: 3.587A pdb=" N THR D 199 " --> pdb=" O ASN D 196 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 200 " --> pdb=" O ARG D 197 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE D 201 " --> pdb=" O ASP D 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 196 through 201' Processing helix chain 'D' and resid 246 through 259 Processing helix chain 'D' and resid 264 through 268 removed outlier: 3.693A 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 318 Processing helix chain 'D' and resid 325 through 336 removed outlier: 3.590A pdb=" N GLY D 329 " --> pdb=" O GLY D 325 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 356 Processing helix chain 'D' and resid 373 through 386 removed outlier: 3.509A pdb=" N CYS D 385 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY D 386 " --> pdb=" O VAL D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 392 No H-bonds generated for 'chain 'D' and resid 390 through 392' Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 406 through 413 Processing helix chain 'D' and resid 421 through 435 removed outlier: 4.353A pdb=" N ALA D 427 " --> pdb=" O PHE D 423 " (cutoff:3.500A) removed outlier: 4.897A 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 450 through 455 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: 3.880A pdb=" N VAL D 506 " --> pdb=" O ASP D 502 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D 510 " --> pdb=" O VAL D 506 " (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 607 through 634 Processing helix chain 'D' and resid 634 through 644 removed outlier: 3.901A 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: 3.921A pdb=" N GLN D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 682 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 906 removed outlier: 3.839A pdb=" N LEU D 906 " --> pdb=" O PHE D 902 " (cutoff:3.500A) Processing helix chain 'D' and resid 907 through 912 Processing helix chain 'D' and resid 916 through 926 Processing helix chain 'D' and resid 926 through 953 Processing helix chain 'D' and resid 958 through 967 Processing helix chain 'D' and resid 967 through 975 removed outlier: 3.621A pdb=" N ILE D 974 " --> pdb=" O PRO D 970 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE D 975 " --> pdb=" O TYR D 971 " (cutoff:3.500A) Processing helix chain 'D' and resid 979 through 984 removed outlier: 3.640A pdb=" N MET D 983 " --> pdb=" O PRO D 979 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 988 Processing helix chain 'D' and resid 1016 through 1033 removed outlier: 3.996A 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: 4.104A pdb=" N TYR D1063 " --> pdb=" O LYS D1059 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG D1064 " --> pdb=" O ALA D1060 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER D1071 " --> pdb=" O ARG D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1079 through 1088 removed outlier: 4.103A pdb=" N SER D1083 " --> pdb=" O PHE D1079 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1142 Processing helix chain 'D' and resid 1143 through 1177 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 77 removed outlier: 6.498A pdb=" N ASN A 89 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU A 234 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU A 91 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ASP A 236 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU A 93 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA A 185 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N PHE A 233 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLY A 187 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL A 235 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA A 189 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ILE A 153 " --> pdb=" O MET A 186 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL A 188 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR A 155 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLY A 156 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N LEU A 299 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU A 275 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL A 301 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LEU A 277 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N CYS A 298 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N TYR A 364 " --> pdb=" O CYS A 298 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU A 300 " --> pdb=" O TYR A 364 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 80 removed outlier: 7.431A pdb=" N ASP A 79 " --> pdb=" O TYR A 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 989 through 990 removed outlier: 4.174A pdb=" N GLU A 989 " --> pdb=" O HIS A1002 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 19 Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 77 removed outlier: 6.498A pdb=" N ASN B 89 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU B 234 " --> pdb=" O ASN B 89 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU B 91 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ASP B 236 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU B 93 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA B 185 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N PHE B 233 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLY B 187 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL B 235 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA B 189 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ILE B 153 " --> pdb=" O MET B 186 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL B 188 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR B 155 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLY B 156 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N LEU B 299 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU B 275 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL B 301 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LEU B 277 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N CYS B 298 " --> pdb=" O THR B 362 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N TYR B 364 " --> pdb=" O CYS B 298 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU B 300 " --> pdb=" O TYR B 364 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.431A pdb=" N ASP B 79 " --> pdb=" O TYR B 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 989 through 990 removed outlier: 4.173A pdb=" N GLU B 989 " --> pdb=" O HIS B1002 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 16 through 19 Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 77 removed outlier: 6.497A pdb=" N ASN C 89 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU C 234 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU C 91 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ASP C 236 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU C 93 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA C 185 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N PHE C 233 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLY C 187 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL C 235 " --> pdb=" O GLY C 187 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA C 189 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE C 153 " --> pdb=" O MET C 186 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL C 188 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR C 155 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N GLY C 156 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N LEU C 299 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU C 275 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL C 301 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LEU C 277 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N CYS C 298 " --> pdb=" O THR C 362 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N TYR C 364 " --> pdb=" O CYS C 298 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU C 300 " --> pdb=" O TYR C 364 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 79 through 80 removed outlier: 7.431A pdb=" N ASP C 79 " --> pdb=" O TYR C 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 989 through 990 removed outlier: 4.174A pdb=" N GLU C 989 " --> pdb=" O HIS C1002 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 16 through 19 Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 77 removed outlier: 6.498A pdb=" N ASN D 89 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU D 234 " --> pdb=" O ASN D 89 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU D 91 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ASP D 236 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU D 93 " --> pdb=" O ASP D 236 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ALA D 185 " --> pdb=" O ALA D 231 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N PHE D 233 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLY D 187 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL D 235 " --> pdb=" O GLY D 187 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA D 189 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ILE D 153 " --> pdb=" O MET D 186 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL D 188 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR D 155 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLY D 156 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N LEU D 299 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU D 275 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL D 301 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU D 277 " --> pdb=" O VAL D 301 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N CYS D 298 " --> pdb=" O THR D 362 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N TYR D 364 " --> pdb=" O CYS D 298 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU D 300 " --> pdb=" O TYR D 364 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 79 through 80 removed outlier: 7.430A pdb=" N ASP D 79 " --> pdb=" O TYR D 211 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 989 through 990 removed outlier: 4.175A pdb=" N GLU D 989 " --> pdb=" O HIS D1002 " (cutoff:3.500A) 1892 hydrogen bonds defined for protein. 5544 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: 12.96 Time building geometry restraints manager: 9.59 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: 9827 1.34 - 1.46: 7136 1.46 - 1.58: 13757 1.58 - 1.69: 0 1.69 - 1.81: 228 Bond restraints: 30948 Sorted by residual: bond pdb=" CB PRO A 40 " pdb=" CG PRO A 40 " ideal model delta sigma weight residual 1.492 1.563 -0.071 5.00e-02 4.00e+02 1.99e+00 bond pdb=" CB PRO D 40 " pdb=" CG PRO D 40 " ideal model delta sigma weight residual 1.492 1.562 -0.070 5.00e-02 4.00e+02 1.96e+00 bond pdb=" CB PRO B 40 " pdb=" CG PRO B 40 " ideal model delta sigma weight residual 1.492 1.562 -0.070 5.00e-02 4.00e+02 1.94e+00 bond pdb=" CB PRO C 40 " pdb=" CG PRO C 40 " ideal model delta sigma weight residual 1.492 1.561 -0.069 5.00e-02 4.00e+02 1.93e+00 bond pdb=" CB ASP D 614 " pdb=" CG ASP D 614 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.21e+00 ... (remaining 30943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 41658 1.78 - 3.55: 341 3.55 - 5.33: 65 5.33 - 7.10: 8 7.10 - 8.88: 12 Bond angle restraints: 42084 Sorted by residual: angle pdb=" N VAL A 221 " pdb=" CA VAL A 221 " pdb=" C VAL A 221 " ideal model delta sigma weight residual 113.53 109.19 4.34 9.80e-01 1.04e+00 1.96e+01 angle pdb=" N VAL B 221 " pdb=" CA VAL B 221 " pdb=" C VAL B 221 " ideal model delta sigma weight residual 113.53 109.21 4.32 9.80e-01 1.04e+00 1.94e+01 angle pdb=" N VAL C 221 " pdb=" CA VAL C 221 " pdb=" C VAL C 221 " ideal model delta sigma weight residual 113.53 109.22 4.31 9.80e-01 1.04e+00 1.93e+01 angle pdb=" N VAL D 221 " pdb=" CA VAL D 221 " pdb=" C VAL D 221 " ideal model delta sigma weight residual 113.53 109.26 4.27 9.80e-01 1.04e+00 1.90e+01 angle pdb=" CB MET D 509 " pdb=" CG MET D 509 " pdb=" SD MET D 509 " ideal model delta sigma weight residual 112.70 120.94 -8.24 3.00e+00 1.11e-01 7.54e+00 ... (remaining 42079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.97: 16096 11.97 - 23.95: 1376 23.95 - 35.92: 484 35.92 - 47.89: 180 47.89 - 59.86: 60 Dihedral angle restraints: 18196 sinusoidal: 6804 harmonic: 11392 Sorted by residual: dihedral pdb=" CB CYS B 35 " pdb=" SG CYS B 35 " pdb=" SG CYS B 37 " pdb=" CB CYS B 37 " ideal model delta sinusoidal sigma weight residual -86.00 -47.46 -38.54 1 1.00e+01 1.00e-02 2.09e+01 dihedral pdb=" CB CYS D 35 " pdb=" SG CYS D 35 " pdb=" SG CYS D 37 " pdb=" CB CYS D 37 " ideal model delta sinusoidal sigma weight residual -86.00 -47.47 -38.53 1 1.00e+01 1.00e-02 2.09e+01 dihedral pdb=" CB CYS C 35 " pdb=" SG CYS C 35 " pdb=" SG CYS C 37 " pdb=" CB CYS C 37 " ideal model delta sinusoidal sigma weight residual -86.00 -47.47 -38.53 1 1.00e+01 1.00e-02 2.09e+01 ... (remaining 18193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 3379 0.030 - 0.061: 1077 0.061 - 0.091: 237 0.091 - 0.122: 118 0.122 - 0.152: 13 Chirality restraints: 4824 Sorted by residual: chirality pdb=" CG LEU D 477 " pdb=" CB LEU D 477 " pdb=" CD1 LEU D 477 " pdb=" CD2 LEU D 477 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.78e-01 chirality pdb=" CG LEU A 477 " pdb=" CB LEU A 477 " pdb=" CD1 LEU A 477 " pdb=" CD2 LEU A 477 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CG LEU C 477 " pdb=" CB LEU C 477 " pdb=" CD1 LEU C 477 " pdb=" CD2 LEU C 477 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 4821 not shown) Planarity restraints: 5316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 39 " -0.039 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO B 40 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 40 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 40 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 39 " 0.038 5.00e-02 4.00e+02 5.71e-02 5.21e+00 pdb=" N PRO D 40 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 40 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 40 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 39 " 0.038 5.00e-02 4.00e+02 5.68e-02 5.16e+00 pdb=" N PRO C 40 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 40 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 40 " 0.032 5.00e-02 4.00e+02 ... (remaining 5313 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 240 2.60 - 3.17: 25982 3.17 - 3.75: 49234 3.75 - 4.32: 63347 4.32 - 4.90: 107237 Nonbonded interactions: 246040 Sorted by model distance: nonbonded pdb=" O GLU C1169 " pdb=" OH TYR D1168 " model vdw 2.020 3.040 nonbonded pdb=" O GLU B1169 " pdb=" OH TYR C1168 " model vdw 2.025 3.040 nonbonded pdb=" OH TYR A1168 " pdb=" O GLU D1169 " model vdw 2.030 3.040 nonbonded pdb=" O GLU A1169 " pdb=" OH TYR B1168 " model vdw 2.063 3.040 nonbonded pdb=" OH TYR D 75 " pdb=" O PRO D 203 " model vdw 2.283 3.040 ... (remaining 246035 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: 0.23 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: 5.050 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: 0.030 Extract box with map and model: 1.300 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 74.070 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.130 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:3.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 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 : 0.009 0.799 30956 Z= 0.466 Angle : 0.583 30.804 42100 Z= 0.295 Chirality : 0.034 0.152 4824 Planarity : 0.004 0.057 5316 Dihedral : 11.710 59.864 10812 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.73 (0.14), residues: 3900 helix: 2.12 (0.10), residues: 2440 sheet: -1.31 (0.32), residues: 240 loop : -0.31 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B1058 HIS 0.004 0.001 HIS D 44 PHE 0.005 0.001 PHE D 23 TYR 0.005 0.001 TYR A 859 ARG 0.004 0.000 ARG D1147 Details of bonding type rmsd hydrogen bonds : bond 0.19727 ( 1892) hydrogen bonds : angle 6.38185 ( 5544) SS BOND : bond 0.56451 ( 8) SS BOND : angle 18.48606 ( 16) covalent geometry : bond 0.00237 (30948) covalent geometry : angle 0.45778 (42084) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 3.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 576 MET cc_start: 0.9141 (mmm) cc_final: 0.8924 (mmm) REVERT: C 576 MET cc_start: 0.9155 (mmm) cc_final: 0.8867 (mmm) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.4890 time to fit residues: 85.2751 Evaluate side-chains 96 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 2.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 334 optimal weight: 20.0000 chunk 300 optimal weight: 9.9990 chunk 166 optimal weight: 8.9990 chunk 102 optimal weight: 40.0000 chunk 202 optimal weight: 30.0000 chunk 160 optimal weight: 9.9990 chunk 310 optimal weight: 30.0000 chunk 120 optimal weight: 0.6980 chunk 188 optimal weight: 9.9990 chunk 231 optimal weight: 40.0000 chunk 359 optimal weight: 7.9990 overall best weight: 7.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN ** A 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 980 GLN A1007 GLN A1014 GLN B 8 GLN ** B 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 980 GLN B1007 GLN B1014 GLN C 8 GLN ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 980 GLN C1007 GLN C1014 GLN D 8 GLN ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 980 GLN D1007 GLN D1014 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.043536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.031829 restraints weight = 242187.142| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 4.13 r_work: 0.2804 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 30956 Z= 0.275 Angle : 0.586 7.270 42100 Z= 0.304 Chirality : 0.038 0.165 4824 Planarity : 0.004 0.050 5316 Dihedral : 3.494 20.168 4300 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.44 % Allowed : 10.23 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.07 (0.14), residues: 3900 helix: 2.46 (0.10), residues: 2440 sheet: -1.32 (0.32), residues: 236 loop : -0.31 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 772 HIS 0.005 0.001 HIS B1128 PHE 0.012 0.001 PHE C 627 TYR 0.014 0.001 TYR D1168 ARG 0.003 0.000 ARG A1147 Details of bonding type rmsd hydrogen bonds : bond 0.04996 ( 1892) hydrogen bonds : angle 4.53995 ( 5544) SS BOND : bond 0.00469 ( 8) SS BOND : angle 2.66942 ( 16) covalent geometry : bond 0.00599 (30948) covalent geometry : angle 0.58330 (42084) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 3.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 355 MET cc_start: 0.8921 (mmm) cc_final: 0.8705 (mmm) REVERT: D 355 MET cc_start: 0.8899 (mmm) cc_final: 0.8695 (mmm) outliers start: 13 outliers final: 4 residues processed: 108 average time/residue: 0.3973 time to fit residues: 74.6482 Evaluate side-chains 98 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 94 time to evaluate : 3.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain D residue 988 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 304 optimal weight: 40.0000 chunk 261 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 224 optimal weight: 7.9990 chunk 193 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 229 optimal weight: 0.0020 chunk 324 optimal weight: 20.0000 chunk 132 optimal weight: 50.0000 chunk 156 optimal weight: 0.0970 chunk 329 optimal weight: 9.9990 overall best weight: 2.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.044129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.032476 restraints weight = 241187.113| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 4.18 r_work: 0.2836 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30956 Z= 0.128 Angle : 0.476 6.779 42100 Z= 0.245 Chirality : 0.036 0.203 4824 Planarity : 0.004 0.048 5316 Dihedral : 3.470 18.122 4300 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.91 % Allowed : 11.34 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.13 (0.14), residues: 3900 helix: 2.50 (0.10), residues: 2448 sheet: -1.36 (0.31), residues: 236 loop : -0.27 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 772 HIS 0.003 0.001 HIS D 44 PHE 0.011 0.001 PHE C 627 TYR 0.011 0.001 TYR A1168 ARG 0.004 0.000 ARG C 353 Details of bonding type rmsd hydrogen bonds : bond 0.03948 ( 1892) hydrogen bonds : angle 4.19378 ( 5544) SS BOND : bond 0.00402 ( 8) SS BOND : angle 2.25409 ( 16) covalent geometry : bond 0.00275 (30948) covalent geometry : angle 0.47375 (42084) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 3.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 355 MET cc_start: 0.8936 (mmm) cc_final: 0.8681 (mmm) REVERT: A 405 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7922 (ptp-110) REVERT: B 355 MET cc_start: 0.9039 (mmm) cc_final: 0.8718 (mmm) REVERT: C 355 MET cc_start: 0.9048 (mmm) cc_final: 0.8784 (mmm) REVERT: D 355 MET cc_start: 0.9046 (mmm) cc_final: 0.8786 (mmm) outliers start: 27 outliers final: 7 residues processed: 120 average time/residue: 0.4044 time to fit residues: 82.5411 Evaluate side-chains 102 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 3.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 988 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 200 optimal weight: 0.4980 chunk 169 optimal weight: 8.9990 chunk 138 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 311 optimal weight: 30.0000 chunk 201 optimal weight: 50.0000 chunk 320 optimal weight: 0.7980 chunk 379 optimal weight: 4.9990 chunk 33 optimal weight: 30.0000 chunk 26 optimal weight: 9.9990 overall best weight: 4.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.043856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.032167 restraints weight = 244435.451| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 4.15 r_work: 0.2820 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 30956 Z= 0.167 Angle : 0.497 8.762 42100 Z= 0.251 Chirality : 0.036 0.139 4824 Planarity : 0.004 0.050 5316 Dihedral : 3.441 19.234 4300 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.45 % Allowed : 11.24 % Favored : 87.31 % 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: 2.23 (0.14), residues: 3900 helix: 2.58 (0.10), residues: 2448 sheet: -1.27 (0.31), residues: 236 loop : -0.23 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 772 HIS 0.003 0.001 HIS D1128 PHE 0.013 0.001 PHE C 627 TYR 0.008 0.001 TYR A1168 ARG 0.002 0.000 ARG B 892 Details of bonding type rmsd hydrogen bonds : bond 0.03679 ( 1892) hydrogen bonds : angle 4.08346 ( 5544) SS BOND : bond 0.00425 ( 8) SS BOND : angle 2.08475 ( 16) covalent geometry : bond 0.00369 (30948) covalent geometry : angle 0.49592 (42084) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 94 time to evaluate : 3.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 355 MET cc_start: 0.9139 (mmm) cc_final: 0.8817 (mmm) REVERT: C 355 MET cc_start: 0.9085 (mmm) cc_final: 0.8807 (mmm) REVERT: C 670 ASP cc_start: 0.9427 (m-30) cc_final: 0.9100 (t0) REVERT: D 355 MET cc_start: 0.9141 (mmm) cc_final: 0.8803 (mmm) REVERT: D 670 ASP cc_start: 0.9395 (m-30) cc_final: 0.9105 (t0) outliers start: 43 outliers final: 22 residues processed: 136 average time/residue: 0.4253 time to fit residues: 99.4245 Evaluate side-chains 119 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 3.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 1164 HIS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 1164 HIS Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 1164 HIS Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 405 ARG Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1164 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 136 optimal weight: 20.0000 chunk 193 optimal weight: 0.9980 chunk 162 optimal weight: 6.9990 chunk 174 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 366 optimal weight: 20.0000 chunk 155 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 369 optimal weight: 9.9990 chunk 231 optimal weight: 40.0000 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.043450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.031764 restraints weight = 244155.298| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 4.16 r_work: 0.2803 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 30956 Z= 0.236 Angle : 0.547 7.998 42100 Z= 0.276 Chirality : 0.037 0.173 4824 Planarity : 0.004 0.051 5316 Dihedral : 3.516 19.951 4300 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.04 % Allowed : 12.08 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.21 (0.14), residues: 3900 helix: 2.55 (0.10), residues: 2472 sheet: -1.26 (0.33), residues: 228 loop : -0.28 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 772 HIS 0.005 0.001 HIS C1128 PHE 0.015 0.001 PHE C 627 TYR 0.008 0.001 TYR A1015 ARG 0.002 0.000 ARG C1138 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 1892) hydrogen bonds : angle 4.16024 ( 5544) SS BOND : bond 0.00440 ( 8) SS BOND : angle 1.92385 ( 16) covalent geometry : bond 0.00520 (30948) covalent geometry : angle 0.54585 (42084) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 3.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 670 ASP cc_start: 0.9372 (m-30) cc_final: 0.9119 (t0) REVERT: B 355 MET cc_start: 0.9113 (mmm) cc_final: 0.8810 (mmm) REVERT: C 355 MET cc_start: 0.9135 (mmm) cc_final: 0.8851 (mmm) REVERT: C 670 ASP cc_start: 0.9414 (m-30) cc_final: 0.9135 (t0) REVERT: D 355 MET cc_start: 0.9167 (mmm) cc_final: 0.8876 (mmm) REVERT: D 670 ASP cc_start: 0.9389 (m-30) cc_final: 0.9086 (t0) outliers start: 31 outliers final: 27 residues processed: 127 average time/residue: 0.4252 time to fit residues: 92.3153 Evaluate side-chains 125 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 3.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 1164 HIS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain B residue 1164 HIS Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 1164 HIS Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 405 ARG Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 876 LEU Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1148 LEU Chi-restraints excluded: chain D residue 1164 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 294 optimal weight: 0.9990 chunk 226 optimal weight: 9.9990 chunk 195 optimal weight: 0.9990 chunk 189 optimal weight: 4.9990 chunk 321 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 233 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 chunk 225 optimal weight: 20.0000 chunk 382 optimal weight: 0.6980 chunk 203 optimal weight: 50.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.044251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.032663 restraints weight = 237523.624| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 4.11 r_work: 0.2845 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 30956 Z= 0.106 Angle : 0.462 8.998 42100 Z= 0.235 Chirality : 0.035 0.140 4824 Planarity : 0.004 0.049 5316 Dihedral : 3.438 18.289 4300 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.94 % Allowed : 12.28 % Favored : 86.78 % 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: 2.34 (0.14), residues: 3900 helix: 2.63 (0.10), residues: 2472 sheet: -0.74 (0.30), residues: 268 loop : -0.27 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 772 HIS 0.003 0.000 HIS C 44 PHE 0.011 0.001 PHE D 627 TYR 0.007 0.001 TYR D1168 ARG 0.002 0.000 ARG B 892 Details of bonding type rmsd hydrogen bonds : bond 0.03382 ( 1892) hydrogen bonds : angle 3.97530 ( 5544) SS BOND : bond 0.00329 ( 8) SS BOND : angle 1.82168 ( 16) covalent geometry : bond 0.00225 (30948) covalent geometry : angle 0.46070 (42084) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 3.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 670 ASP cc_start: 0.9397 (m-30) cc_final: 0.9083 (t0) REVERT: B 355 MET cc_start: 0.9075 (mmm) cc_final: 0.8820 (mmm) REVERT: C 670 ASP cc_start: 0.9431 (m-30) cc_final: 0.9101 (t0) REVERT: D 355 MET cc_start: 0.9154 (mmm) cc_final: 0.8918 (mmm) REVERT: D 670 ASP cc_start: 0.9375 (m-30) cc_final: 0.9064 (t0) outliers start: 28 outliers final: 23 residues processed: 125 average time/residue: 0.4070 time to fit residues: 86.2785 Evaluate side-chains 121 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 3.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 1164 HIS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 1164 HIS Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1164 HIS Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 405 ARG Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1164 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 225 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 172 optimal weight: 7.9990 chunk 197 optimal weight: 20.0000 chunk 317 optimal weight: 20.0000 chunk 391 optimal weight: 6.9990 chunk 212 optimal weight: 9.9990 chunk 119 optimal weight: 30.0000 chunk 175 optimal weight: 9.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.043306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.031599 restraints weight = 246117.705| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 4.18 r_work: 0.2798 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 30956 Z= 0.301 Angle : 0.605 9.023 42100 Z= 0.302 Chirality : 0.038 0.139 4824 Planarity : 0.004 0.052 5316 Dihedral : 3.555 21.377 4300 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.38 % Allowed : 12.35 % Favored : 86.27 % 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 (0.14), residues: 3900 helix: 2.57 (0.11), residues: 2472 sheet: -1.19 (0.33), residues: 228 loop : -0.29 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 649 HIS 0.006 0.001 HIS C1128 PHE 0.017 0.001 PHE C 627 TYR 0.009 0.001 TYR A 464 ARG 0.002 0.000 ARG A 459 Details of bonding type rmsd hydrogen bonds : bond 0.03864 ( 1892) hydrogen bonds : angle 4.20926 ( 5544) SS BOND : bond 0.00475 ( 8) SS BOND : angle 1.76844 ( 16) covalent geometry : bond 0.00656 (30948) covalent geometry : angle 0.60406 (42084) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 97 time to evaluate : 8.000 Fit side-chains revert: symmetry clash REVERT: A 670 ASP cc_start: 0.9415 (m-30) cc_final: 0.9156 (t0) REVERT: B 355 MET cc_start: 0.9092 (mmm) cc_final: 0.8840 (mmm) REVERT: C 355 MET cc_start: 0.9130 (mmm) cc_final: 0.8918 (mmm) REVERT: C 670 ASP cc_start: 0.9446 (m-30) cc_final: 0.9151 (t0) REVERT: D 355 MET cc_start: 0.9177 (mmm) cc_final: 0.8945 (mmm) REVERT: D 670 ASP cc_start: 0.9413 (m-30) cc_final: 0.9180 (t0) outliers start: 41 outliers final: 29 residues processed: 137 average time/residue: 0.6183 time to fit residues: 149.1473 Evaluate side-chains 126 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 8.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 1164 HIS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1164 HIS Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1164 HIS Chi-restraints excluded: chain D residue 405 ARG Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 876 LEU Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1127 VAL Chi-restraints excluded: chain D residue 1164 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 77 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 367 optimal weight: 7.9990 chunk 199 optimal weight: 50.0000 chunk 185 optimal weight: 0.9990 chunk 289 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 5 optimal weight: 30.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.043966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.032277 restraints weight = 240730.759| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 4.18 r_work: 0.2832 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 30956 Z= 0.132 Angle : 0.488 10.167 42100 Z= 0.247 Chirality : 0.036 0.140 4824 Planarity : 0.004 0.050 5316 Dihedral : 3.491 19.133 4300 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.04 % Allowed : 12.92 % Favored : 86.04 % 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: 2.32 (0.14), residues: 3900 helix: 2.64 (0.10), residues: 2472 sheet: -1.16 (0.33), residues: 228 loop : -0.27 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 772 HIS 0.003 0.001 HIS C1128 PHE 0.011 0.001 PHE D 627 TYR 0.006 0.001 TYR D1168 ARG 0.002 0.000 ARG D 92 Details of bonding type rmsd hydrogen bonds : bond 0.03473 ( 1892) hydrogen bonds : angle 4.02005 ( 5544) SS BOND : bond 0.00306 ( 8) SS BOND : angle 1.73202 ( 16) covalent geometry : bond 0.00290 (30948) covalent geometry : angle 0.48684 (42084) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 3.411 Fit side-chains revert: symmetry clash REVERT: A 670 ASP cc_start: 0.9419 (m-30) cc_final: 0.9132 (t0) REVERT: B 355 MET cc_start: 0.9103 (mmm) cc_final: 0.8855 (mmm) REVERT: C 355 MET cc_start: 0.9157 (mmm) cc_final: 0.8945 (mmm) REVERT: C 670 ASP cc_start: 0.9421 (m-30) cc_final: 0.9105 (t0) REVERT: D 355 MET cc_start: 0.9157 (mmm) cc_final: 0.8923 (mmm) REVERT: D 670 ASP cc_start: 0.9393 (m-30) cc_final: 0.9110 (t0) outliers start: 31 outliers final: 30 residues processed: 127 average time/residue: 0.3907 time to fit residues: 85.5322 Evaluate side-chains 127 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 3.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 1164 HIS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1164 HIS Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 648 LEU Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1164 HIS Chi-restraints excluded: chain D residue 405 ARG Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 876 LEU Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1164 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 27 optimal weight: 0.0270 chunk 329 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 371 optimal weight: 0.9980 chunk 193 optimal weight: 10.0000 chunk 218 optimal weight: 30.0000 chunk 340 optimal weight: 0.6980 chunk 4 optimal weight: 50.0000 chunk 322 optimal weight: 1.9990 chunk 209 optimal weight: 20.0000 chunk 75 optimal weight: 4.9990 overall best weight: 1.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.044391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.032837 restraints weight = 238279.370| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 4.17 r_work: 0.2854 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 30956 Z= 0.099 Angle : 0.471 11.096 42100 Z= 0.236 Chirality : 0.035 0.141 4824 Planarity : 0.004 0.049 5316 Dihedral : 3.384 17.797 4300 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.74 % Allowed : 13.29 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.39 (0.14), residues: 3900 helix: 2.68 (0.10), residues: 2468 sheet: -1.06 (0.33), residues: 228 loop : -0.22 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 772 HIS 0.003 0.000 HIS A 44 PHE 0.011 0.001 PHE D 627 TYR 0.006 0.001 TYR D1168 ARG 0.002 0.000 ARG C 892 Details of bonding type rmsd hydrogen bonds : bond 0.03186 ( 1892) hydrogen bonds : angle 3.90817 ( 5544) SS BOND : bond 0.00247 ( 8) SS BOND : angle 1.73617 ( 16) covalent geometry : bond 0.00214 (30948) covalent geometry : angle 0.47027 (42084) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 4.410 Fit side-chains revert: symmetry clash REVERT: A 670 ASP cc_start: 0.9397 (m-30) cc_final: 0.9106 (t0) REVERT: B 355 MET cc_start: 0.9115 (mmm) cc_final: 0.8880 (mmm) REVERT: B 405 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.8056 (ptp-110) REVERT: C 355 MET cc_start: 0.9146 (mmm) cc_final: 0.8925 (mmm) REVERT: C 670 ASP cc_start: 0.9430 (m-30) cc_final: 0.9096 (t0) REVERT: D 355 MET cc_start: 0.9172 (mmm) cc_final: 0.8935 (mmm) REVERT: D 670 ASP cc_start: 0.9373 (m-30) cc_final: 0.9090 (t0) outliers start: 22 outliers final: 18 residues processed: 120 average time/residue: 0.4948 time to fit residues: 102.2924 Evaluate side-chains 118 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 5.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1164 HIS Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 1164 HIS Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1164 HIS Chi-restraints excluded: chain D residue 405 ARG Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 876 LEU Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1164 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 23 optimal weight: 3.9990 chunk 394 optimal weight: 20.0000 chunk 287 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 301 optimal weight: 50.0000 chunk 361 optimal weight: 4.9990 chunk 275 optimal weight: 10.0000 chunk 273 optimal weight: 9.9990 chunk 317 optimal weight: 8.9990 chunk 128 optimal weight: 40.0000 chunk 6 optimal weight: 30.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.043353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.031772 restraints weight = 246310.221| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 4.14 r_work: 0.2803 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 30956 Z= 0.270 Angle : 0.581 10.001 42100 Z= 0.292 Chirality : 0.038 0.142 4824 Planarity : 0.004 0.051 5316 Dihedral : 3.498 20.929 4300 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.81 % Allowed : 13.32 % Favored : 85.87 % 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: 2.32 (0.14), residues: 3900 helix: 2.63 (0.11), residues: 2472 sheet: -0.72 (0.31), residues: 268 loop : -0.34 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 649 HIS 0.005 0.001 HIS C1128 PHE 0.015 0.001 PHE B 627 TYR 0.011 0.001 TYR A1015 ARG 0.004 0.000 ARG C 197 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 1892) hydrogen bonds : angle 4.11610 ( 5544) SS BOND : bond 0.00452 ( 8) SS BOND : angle 1.74996 ( 16) covalent geometry : bond 0.00587 (30948) covalent geometry : angle 0.58021 (42084) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 4.474 Fit side-chains revert: symmetry clash REVERT: A 670 ASP cc_start: 0.9398 (m-30) cc_final: 0.9128 (t0) REVERT: B 355 MET cc_start: 0.9128 (mmm) cc_final: 0.8893 (mmm) REVERT: B 405 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8053 (ptp-110) REVERT: C 355 MET cc_start: 0.9187 (mmm) cc_final: 0.8973 (mmm) REVERT: C 670 ASP cc_start: 0.9430 (m-30) cc_final: 0.9154 (t0) REVERT: D 355 MET cc_start: 0.9175 (mmm) cc_final: 0.8945 (mmm) REVERT: D 622 MET cc_start: 0.9035 (ptp) cc_final: 0.8810 (ptt) REVERT: D 670 ASP cc_start: 0.9413 (m-30) cc_final: 0.9148 (t0) outliers start: 24 outliers final: 21 residues processed: 122 average time/residue: 0.6038 time to fit residues: 128.7873 Evaluate side-chains 119 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 5.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 789 SER Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1164 HIS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 1164 HIS Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 789 SER Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1164 HIS Chi-restraints excluded: chain D residue 405 ARG Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 876 LEU Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1164 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 286 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 142 optimal weight: 2.9990 chunk 386 optimal weight: 7.9990 chunk 350 optimal weight: 5.9990 chunk 306 optimal weight: 7.9990 chunk 109 optimal weight: 0.1980 chunk 102 optimal weight: 0.5980 chunk 95 optimal weight: 9.9990 chunk 284 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.044116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.032627 restraints weight = 238905.745| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 4.16 r_work: 0.2840 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 30956 Z= 0.107 Angle : 0.479 10.369 42100 Z= 0.241 Chirality : 0.035 0.139 4824 Planarity : 0.004 0.049 5316 Dihedral : 3.434 18.476 4300 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.74 % Allowed : 13.53 % Favored : 85.73 % 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: 2.40 (0.14), residues: 3900 helix: 2.69 (0.10), residues: 2464 sheet: -0.66 (0.31), residues: 268 loop : -0.30 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 772 HIS 0.003 0.001 HIS A 44 PHE 0.011 0.001 PHE D 627 TYR 0.006 0.001 TYR A1063 ARG 0.002 0.000 ARG A1150 Details of bonding type rmsd hydrogen bonds : bond 0.03330 ( 1892) hydrogen bonds : angle 3.94591 ( 5544) SS BOND : bond 0.00232 ( 8) SS BOND : angle 1.69356 ( 16) covalent geometry : bond 0.00232 (30948) covalent geometry : angle 0.47816 (42084) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17493.54 seconds wall clock time: 314 minutes 54.78 seconds (18894.78 seconds total)