Starting phenix.real_space_refine on Mon Aug 25 20:10:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b8w_44360/08_2025/9b8w_44360.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b8w_44360/08_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_44360/08_2025/9b8w_44360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b8w_44360/08_2025/9b8w_44360.map" model { file = "/net/cci-nas-00/data/ceres_data/9b8w_44360/08_2025/9b8w_44360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b8w_44360/08_2025/9b8w_44360.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 15, 'GLN:plan1': 4, 'ARG:plan': 12, 'ASP:plan': 15, 'HIS:plan': 2, 'PHE:plan': 4, 'ASN:plan1': 1} 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: B, C, D Time building chain proxies: 6.42, per 1000 atoms: 0.21 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 B 35 " - pdb=" SG CYS B 37 " distance=2.83 Simple disulfide: pdb=" SG CYS C 35 " - pdb=" SG CYS C 37 " distance=2.83 Simple disulfide: pdb=" SG CYS D 35 " - pdb=" SG CYS D 37 " distance=2.83 Simple disulfide: pdb=" SG CYS B 993 " - pdb=" SG CYS B1011 " distance=2.03 Simple disulfide: pdb=" SG CYS C 993 " - pdb=" SG CYS C1011 " 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: 2.45 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.90 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: 5.82 Time building geometry restraints manager: 3.33 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 25.660 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.840 ------------------------------------------------------------------------------- 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 : 6.64 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.004 0.000 ARG D1147 TYR 0.005 0.001 TYR A 859 PHE 0.005 0.001 PHE D 23 TRP 0.006 0.001 TRP B1058 HIS 0.004 0.001 HIS D 44 Details of bonding type rmsd covalent geometry : bond 0.00237 (30948) covalent geometry : angle 0.45778 (42084) SS BOND : bond 0.56451 ( 8) SS BOND : angle 18.48606 ( 16) hydrogen bonds : bond 0.19727 ( 1892) hydrogen bonds : angle 6.38185 ( 5544) *********************** 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 : 1.116 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: 0.1608 time to fit residues: 27.8648 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 : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 197 optimal weight: 40.0000 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 overall best weight: 8.7992 ------------------------------------------------------------------------------- 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 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 = 0.3450 r_free = 0.3450 target = 0.043322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.031593 restraints weight = 244113.690| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 4.17 r_work: 0.2796 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 30956 Z= 0.318 Angle : 0.638 6.913 42100 Z= 0.324 Chirality : 0.040 0.172 4824 Planarity : 0.005 0.053 5316 Dihedral : 3.629 21.201 4300 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.67 % Allowed : 10.70 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.14), residues: 3900 helix: 2.36 (0.10), residues: 2444 sheet: -1.34 (0.32), residues: 236 loop : -0.34 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A1147 TYR 0.013 0.001 TYR D1168 PHE 0.015 0.001 PHE C 627 TRP 0.011 0.001 TRP C 649 HIS 0.006 0.001 HIS B1128 Details of bonding type rmsd covalent geometry : bond 0.00697 (30948) covalent geometry : angle 0.63619 (42084) SS BOND : bond 0.00871 ( 8) SS BOND : angle 2.82807 ( 16) hydrogen bonds : bond 0.04667 ( 1892) hydrogen bonds : angle 4.51260 ( 5544) *********************** 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 116 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 355 MET cc_start: 0.8976 (mmm) cc_final: 0.8751 (mmm) REVERT: D 355 MET cc_start: 0.8951 (mmm) cc_final: 0.8741 (mmm) outliers start: 20 outliers final: 5 residues processed: 115 average time/residue: 0.1657 time to fit residues: 32.3946 Evaluate side-chains 100 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 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 150 optimal weight: 7.9990 chunk 377 optimal weight: 2.9990 chunk 264 optimal weight: 0.0770 chunk 104 optimal weight: 30.0000 chunk 217 optimal weight: 30.0000 chunk 239 optimal weight: 6.9990 chunk 274 optimal weight: 1.9990 chunk 371 optimal weight: 0.8980 chunk 392 optimal weight: 0.8980 chunk 292 optimal weight: 4.9990 chunk 69 optimal weight: 20.0000 overall best weight: 1.3742 ------------------------------------------------------------------------------- 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** ** 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 = 0.044386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.032773 restraints weight = 240498.083| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 4.19 r_work: 0.2847 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30956 Z= 0.099 Angle : 0.468 7.037 42100 Z= 0.240 Chirality : 0.036 0.166 4824 Planarity : 0.004 0.047 5316 Dihedral : 3.485 17.322 4300 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.01 % Allowed : 11.00 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.14), residues: 3900 helix: 2.50 (0.10), residues: 2444 sheet: -1.36 (0.31), residues: 236 loop : -0.33 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 353 TYR 0.010 0.001 TYR A1168 PHE 0.009 0.001 PHE A 627 TRP 0.012 0.001 TRP A 772 HIS 0.004 0.001 HIS D 44 Details of bonding type rmsd covalent geometry : bond 0.00197 (30948) covalent geometry : angle 0.46632 (42084) SS BOND : bond 0.00429 ( 8) SS BOND : angle 2.28292 ( 16) hydrogen bonds : bond 0.03809 ( 1892) hydrogen bonds : angle 4.14696 ( 5544) *********************** 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 125 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 MET cc_start: 0.8960 (mmm) cc_final: 0.8702 (mmm) REVERT: A 405 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7947 (ptp-110) REVERT: B 355 MET cc_start: 0.9051 (mmm) cc_final: 0.8721 (mmm) REVERT: C 355 MET cc_start: 0.9002 (mmm) cc_final: 0.8724 (mmm) REVERT: D 355 MET cc_start: 0.9055 (mmm) cc_final: 0.8762 (mmm) outliers start: 30 outliers final: 8 residues processed: 124 average time/residue: 0.1990 time to fit residues: 41.1305 Evaluate side-chains 104 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 C residue 829 LEU Chi-restraints excluded: chain C residue 1164 HIS Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1164 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 211 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 246 optimal weight: 9.9990 chunk 371 optimal weight: 7.9990 chunk 222 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 330 optimal weight: 40.0000 chunk 252 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 221 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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** ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 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** ** 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 = 0.3446 r_free = 0.3446 target = 0.043230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.031595 restraints weight = 245586.390| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 4.15 r_work: 0.2794 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 30956 Z= 0.282 Angle : 0.598 8.322 42100 Z= 0.298 Chirality : 0.038 0.144 4824 Planarity : 0.004 0.052 5316 Dihedral : 3.571 21.097 4300 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.18 % Allowed : 11.34 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.08 (0.14), residues: 3900 helix: 2.46 (0.10), residues: 2468 sheet: -1.32 (0.33), residues: 228 loop : -0.37 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1147 TYR 0.009 0.001 TYR A1015 PHE 0.017 0.001 PHE B 627 TRP 0.010 0.001 TRP C 649 HIS 0.006 0.001 HIS C1128 Details of bonding type rmsd covalent geometry : bond 0.00619 (30948) covalent geometry : angle 0.59708 (42084) SS BOND : bond 0.00541 ( 8) SS BOND : angle 2.11076 ( 16) hydrogen bonds : bond 0.04006 ( 1892) hydrogen bonds : angle 4.26369 ( 5544) *********************** 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 130 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 MET cc_start: 0.9096 (mmm) cc_final: 0.8826 (mmm) REVERT: B 355 MET cc_start: 0.9116 (mmm) cc_final: 0.8817 (mmm) REVERT: B 670 ASP cc_start: 0.9394 (m-30) cc_final: 0.9130 (t0) REVERT: C 355 MET cc_start: 0.9110 (mmm) cc_final: 0.8836 (mmm) REVERT: C 670 ASP cc_start: 0.9444 (m-30) cc_final: 0.9134 (t0) REVERT: D 355 MET cc_start: 0.9168 (mmm) cc_final: 0.8845 (mmm) REVERT: D 670 ASP cc_start: 0.9423 (m-30) cc_final: 0.9140 (t0) outliers start: 35 outliers final: 23 residues processed: 129 average time/residue: 0.1974 time to fit residues: 42.6233 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 : 1.203 ------------------------------------------------------------------------------- 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 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 347 LEU Chi-restraints excluded: chain D residue 405 ARG Chi-restraints excluded: chain D residue 648 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 394 optimal weight: 6.9990 chunk 259 optimal weight: 10.0000 chunk 219 optimal weight: 4.9990 chunk 346 optimal weight: 7.9990 chunk 179 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 291 optimal weight: 6.9990 chunk 260 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 44 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 = 0.3459 r_free = 0.3459 target = 0.043598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.032065 restraints weight = 243468.067| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 4.08 r_work: 0.2813 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 30956 Z= 0.179 Angle : 0.505 8.199 42100 Z= 0.257 Chirality : 0.036 0.143 4824 Planarity : 0.004 0.050 5316 Dihedral : 3.523 19.544 4300 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.08 % Allowed : 12.11 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.14), residues: 3900 helix: 2.56 (0.10), residues: 2472 sheet: -1.30 (0.33), residues: 228 loop : -0.34 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 892 TYR 0.008 0.001 TYR D1168 PHE 0.012 0.001 PHE C 627 TRP 0.011 0.001 TRP A 772 HIS 0.004 0.001 HIS B1128 Details of bonding type rmsd covalent geometry : bond 0.00393 (30948) covalent geometry : angle 0.50376 (42084) SS BOND : bond 0.00413 ( 8) SS BOND : angle 2.00964 ( 16) hydrogen bonds : bond 0.03675 ( 1892) hydrogen bonds : angle 4.12373 ( 5544) *********************** 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 131 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 355 MET cc_start: 0.9106 (mmm) cc_final: 0.8785 (mmm) REVERT: B 670 ASP cc_start: 0.9397 (m-30) cc_final: 0.9152 (t0) REVERT: C 355 MET cc_start: 0.9113 (mmm) cc_final: 0.8815 (mmm) REVERT: C 670 ASP cc_start: 0.9435 (m-30) cc_final: 0.9126 (t0) REVERT: D 355 MET cc_start: 0.9184 (mmm) cc_final: 0.8902 (mmm) REVERT: D 670 ASP cc_start: 0.9411 (m-30) cc_final: 0.9114 (t0) outliers start: 32 outliers final: 24 residues processed: 130 average time/residue: 0.2039 time to fit residues: 44.0426 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 : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 311 LEU 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 405 ARG Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 1127 VAL 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 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 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 988 MET 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 167 optimal weight: 9.9990 chunk 331 optimal weight: 9.9990 chunk 206 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 283 optimal weight: 2.9990 chunk 347 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 272 optimal weight: 4.9990 chunk 257 optimal weight: 6.9990 chunk 310 optimal weight: 0.9990 chunk 314 optimal weight: 40.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.3465 r_free = 0.3465 target = 0.043695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.031989 restraints weight = 241279.694| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 4.17 r_work: 0.2816 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.1707 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= 0.196 Angle : 0.514 8.419 42100 Z= 0.260 Chirality : 0.036 0.142 4824 Planarity : 0.004 0.051 5316 Dihedral : 3.510 20.068 4300 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.45 % Allowed : 11.94 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.22 (0.14), residues: 3900 helix: 2.58 (0.10), residues: 2472 sheet: -1.28 (0.33), residues: 228 loop : -0.34 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 892 TYR 0.007 0.001 TYR D1168 PHE 0.013 0.001 PHE D 627 TRP 0.011 0.001 TRP A 772 HIS 0.004 0.001 HIS C1128 Details of bonding type rmsd covalent geometry : bond 0.00431 (30948) covalent geometry : angle 0.51238 (42084) SS BOND : bond 0.00404 ( 8) SS BOND : angle 1.91332 ( 16) hydrogen bonds : bond 0.03627 ( 1892) hydrogen bonds : angle 4.09749 ( 5544) *********************** 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 141 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 98 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 355 MET cc_start: 0.9082 (mmm) cc_final: 0.8871 (mmm) REVERT: A 670 ASP cc_start: 0.9420 (m-30) cc_final: 0.9138 (t0) REVERT: B 355 MET cc_start: 0.9102 (mmm) cc_final: 0.8859 (mmm) REVERT: B 670 ASP cc_start: 0.9418 (m-30) cc_final: 0.9166 (t0) REVERT: C 670 ASP cc_start: 0.9435 (m-30) cc_final: 0.9118 (t0) REVERT: D 309 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.8258 (m-30) REVERT: D 355 MET cc_start: 0.9199 (mmm) cc_final: 0.8981 (mmm) REVERT: D 670 ASP cc_start: 0.9410 (m-30) cc_final: 0.9124 (t0) outliers start: 43 outliers final: 29 residues processed: 139 average time/residue: 0.1903 time to fit residues: 44.9257 Evaluate side-chains 128 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 311 LEU 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 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 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 988 MET Chi-restraints excluded: chain C residue 1127 VAL 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 876 LEU Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1127 VAL Chi-restraints excluded: chain D residue 1148 LEU 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 245 optimal weight: 8.9990 chunk 291 optimal weight: 8.9990 chunk 373 optimal weight: 0.9980 chunk 307 optimal weight: 0.4980 chunk 9 optimal weight: 5.9990 chunk 354 optimal weight: 4.9990 chunk 200 optimal weight: 20.0000 chunk 199 optimal weight: 50.0000 chunk 367 optimal weight: 7.9990 chunk 388 optimal weight: 0.9980 chunk 386 optimal weight: 2.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.044232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.032576 restraints weight = 240162.362| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 4.19 r_work: 0.2841 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1794 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= 0.108 Angle : 0.471 9.352 42100 Z= 0.239 Chirality : 0.035 0.142 4824 Planarity : 0.004 0.049 5316 Dihedral : 3.467 18.351 4300 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.24 % Allowed : 12.75 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.29 (0.14), residues: 3900 helix: 2.63 (0.10), residues: 2472 sheet: -0.77 (0.30), residues: 268 loop : -0.37 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 892 TYR 0.006 0.001 TYR D1168 PHE 0.011 0.001 PHE D 627 TRP 0.012 0.001 TRP A 772 HIS 0.003 0.000 HIS A 44 Details of bonding type rmsd covalent geometry : bond 0.00234 (30948) covalent geometry : angle 0.46924 (42084) SS BOND : bond 0.00324 ( 8) SS BOND : angle 1.86052 ( 16) hydrogen bonds : bond 0.03375 ( 1892) hydrogen bonds : angle 3.97754 ( 5544) *********************** 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 134 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 97 time to evaluate : 1.656 Fit side-chains revert: symmetry clash REVERT: A 309 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8213 (m-30) REVERT: A 355 MET cc_start: 0.9110 (mmm) cc_final: 0.8875 (mmm) REVERT: A 670 ASP cc_start: 0.9419 (m-30) cc_final: 0.9120 (t0) REVERT: B 309 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.7698 (t0) REVERT: B 355 MET cc_start: 0.9103 (mmm) cc_final: 0.8870 (mmm) REVERT: B 670 ASP cc_start: 0.9402 (m-30) cc_final: 0.9152 (t0) REVERT: C 355 MET cc_start: 0.9138 (mmm) cc_final: 0.8915 (mmm) REVERT: C 670 ASP cc_start: 0.9422 (m-30) cc_final: 0.9098 (t0) REVERT: D 355 MET cc_start: 0.9178 (mmm) cc_final: 0.8958 (mmm) REVERT: D 670 ASP cc_start: 0.9402 (m-30) cc_final: 0.9105 (t0) outliers start: 37 outliers final: 29 residues processed: 133 average time/residue: 0.1930 time to fit residues: 44.1524 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 : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 309 ASP 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 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 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 200 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 405 ARG 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 288 ILE Chi-restraints excluded: chain D residue 405 ARG 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 341 optimal weight: 10.0000 chunk 252 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 83 optimal weight: 30.0000 chunk 254 optimal weight: 7.9990 chunk 264 optimal weight: 9.9990 chunk 186 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 295 optimal weight: 20.0000 chunk 263 optimal weight: 4.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 = 0.3448 r_free = 0.3448 target = 0.043345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.031736 restraints weight = 245706.500| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 4.18 r_work: 0.2803 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 30956 Z= 0.258 Angle : 0.573 10.037 42100 Z= 0.286 Chirality : 0.038 0.142 4824 Planarity : 0.004 0.051 5316 Dihedral : 3.538 21.116 4300 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.41 % Allowed : 12.58 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.25 (0.14), residues: 3900 helix: 2.61 (0.11), residues: 2472 sheet: -1.21 (0.33), residues: 228 loop : -0.36 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 892 TYR 0.009 0.001 TYR A1015 PHE 0.016 0.001 PHE C 627 TRP 0.010 0.001 TRP D 649 HIS 0.005 0.001 HIS C1128 Details of bonding type rmsd covalent geometry : bond 0.00564 (30948) covalent geometry : angle 0.57226 (42084) SS BOND : bond 0.00456 ( 8) SS BOND : angle 1.84278 ( 16) hydrogen bonds : bond 0.03748 ( 1892) hydrogen bonds : angle 4.14538 ( 5544) *********************** 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 139 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 97 time to evaluate : 1.263 Fit side-chains revert: symmetry clash REVERT: A 355 MET cc_start: 0.9181 (mmm) cc_final: 0.8944 (mmm) REVERT: A 670 ASP cc_start: 0.9387 (m-30) cc_final: 0.9148 (t0) REVERT: B 355 MET cc_start: 0.9138 (mmm) cc_final: 0.8909 (mmm) REVERT: B 670 ASP cc_start: 0.9393 (m-30) cc_final: 0.9150 (t0) REVERT: C 355 MET cc_start: 0.9158 (mmm) cc_final: 0.8921 (mmm) REVERT: C 670 ASP cc_start: 0.9396 (m-30) cc_final: 0.9110 (t0) REVERT: D 355 MET cc_start: 0.9194 (mmm) cc_final: 0.8963 (mmm) REVERT: D 670 ASP cc_start: 0.9389 (m-30) cc_final: 0.9164 (t0) outliers start: 42 outliers final: 35 residues processed: 136 average time/residue: 0.1894 time to fit residues: 44.1350 Evaluate side-chains 132 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 288 ILE 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 1127 VAL Chi-restraints excluded: chain A residue 1164 HIS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 288 ILE 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 988 MET Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1164 HIS Chi-restraints excluded: chain D residue 288 ILE 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 1127 VAL 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 276 optimal weight: 0.9980 chunk 357 optimal weight: 3.9990 chunk 376 optimal weight: 0.7980 chunk 319 optimal weight: 5.9990 chunk 217 optimal weight: 30.0000 chunk 80 optimal weight: 3.9990 chunk 246 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 328 optimal weight: 30.0000 chunk 221 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- 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 = 0.044097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.032517 restraints weight = 241344.586| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 4.20 r_work: 0.2836 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 30956 Z= 0.111 Angle : 0.480 10.209 42100 Z= 0.242 Chirality : 0.036 0.182 4824 Planarity : 0.004 0.049 5316 Dihedral : 3.477 18.714 4300 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.01 % Allowed : 13.22 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.33 (0.14), residues: 3900 helix: 2.66 (0.10), residues: 2464 sheet: -0.71 (0.31), residues: 268 loop : -0.37 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 474 TYR 0.006 0.001 TYR A1063 PHE 0.011 0.001 PHE D 627 TRP 0.012 0.001 TRP A 772 HIS 0.003 0.001 HIS A 44 Details of bonding type rmsd covalent geometry : bond 0.00242 (30948) covalent geometry : angle 0.47921 (42084) SS BOND : bond 0.00271 ( 8) SS BOND : angle 1.82391 ( 16) hydrogen bonds : bond 0.03375 ( 1892) hydrogen bonds : angle 3.97676 ( 5544) *********************** 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 127 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 1.332 Fit side-chains revert: symmetry clash REVERT: A 355 MET cc_start: 0.9189 (mmm) cc_final: 0.8940 (mmm) REVERT: A 670 ASP cc_start: 0.9364 (m-30) cc_final: 0.9104 (t0) REVERT: B 355 MET cc_start: 0.9137 (mmm) cc_final: 0.8901 (mmm) REVERT: B 670 ASP cc_start: 0.9380 (m-30) cc_final: 0.9138 (t0) REVERT: C 355 MET cc_start: 0.9160 (mmm) cc_final: 0.8912 (mmm) REVERT: C 670 ASP cc_start: 0.9384 (m-30) cc_final: 0.9081 (t0) REVERT: D 355 MET cc_start: 0.9192 (mmm) cc_final: 0.8965 (mmm) REVERT: D 670 ASP cc_start: 0.9378 (m-30) cc_final: 0.9098 (t0) outliers start: 30 outliers final: 29 residues processed: 126 average time/residue: 0.1962 time to fit residues: 42.1860 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 : 1.355 ------------------------------------------------------------------------------- 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 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 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 288 ILE Chi-restraints excluded: chain C residue 405 ARG 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 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 1127 VAL 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 57 optimal weight: 6.9990 chunk 137 optimal weight: 20.0000 chunk 203 optimal weight: 40.0000 chunk 93 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 332 optimal weight: 7.9990 chunk 251 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 273 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 = 0.3449 r_free = 0.3449 target = 0.043382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.031719 restraints weight = 245880.822| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 4.18 r_work: 0.2806 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 30956 Z= 0.241 Angle : 0.561 10.046 42100 Z= 0.281 Chirality : 0.038 0.148 4824 Planarity : 0.004 0.051 5316 Dihedral : 3.523 21.031 4300 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.11 % Allowed : 13.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.14), residues: 3900 helix: 2.61 (0.11), residues: 2472 sheet: -1.15 (0.34), residues: 228 loop : -0.35 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 892 TYR 0.009 0.001 TYR C 464 PHE 0.015 0.001 PHE C 627 TRP 0.010 0.001 TRP D 649 HIS 0.005 0.001 HIS C1128 Details of bonding type rmsd covalent geometry : bond 0.00528 (30948) covalent geometry : angle 0.56015 (42084) SS BOND : bond 0.00442 ( 8) SS BOND : angle 1.85322 ( 16) hydrogen bonds : bond 0.03702 ( 1892) hydrogen bonds : angle 4.11161 ( 5544) ********************** 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 130 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 1.261 Fit side-chains REVERT: A 355 MET cc_start: 0.9189 (mmm) cc_final: 0.8958 (mmm) REVERT: A 670 ASP cc_start: 0.9392 (m-30) cc_final: 0.9160 (t0) REVERT: B 355 MET cc_start: 0.9114 (mmm) cc_final: 0.8891 (mmm) REVERT: B 405 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8072 (ptp-110) REVERT: B 670 ASP cc_start: 0.9411 (m-30) cc_final: 0.9180 (t0) REVERT: C 355 MET cc_start: 0.9150 (mmm) cc_final: 0.8929 (mmm) REVERT: C 670 ASP cc_start: 0.9408 (m-30) cc_final: 0.9139 (t0) REVERT: D 355 MET cc_start: 0.9184 (mmm) cc_final: 0.8963 (mmm) REVERT: D 670 ASP cc_start: 0.9404 (m-30) cc_final: 0.9165 (t0) outliers start: 33 outliers final: 32 residues processed: 129 average time/residue: 0.1936 time to fit residues: 42.3213 Evaluate side-chains 129 residues out of total 3340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 96 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 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 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 288 ILE 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 876 LEU Chi-restraints excluded: chain C residue 1127 VAL Chi-restraints excluded: chain C residue 1164 HIS Chi-restraints excluded: chain D residue 288 ILE 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 1127 VAL 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 127 optimal weight: 30.0000 chunk 182 optimal weight: 30.0000 chunk 98 optimal weight: 20.0000 chunk 288 optimal weight: 6.9990 chunk 384 optimal weight: 3.9990 chunk 268 optimal weight: 6.9990 chunk 274 optimal weight: 4.9990 chunk 241 optimal weight: 4.9990 chunk 354 optimal weight: 1.9990 chunk 362 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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** ** 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 = 0.3466 r_free = 0.3466 target = 0.043853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.032257 restraints weight = 242930.247| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 4.18 r_work: 0.2826 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 30956 Z= 0.138 Angle : 0.494 10.396 42100 Z= 0.248 Chirality : 0.036 0.152 4824 Planarity : 0.004 0.050 5316 Dihedral : 3.485 19.421 4300 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.14 % Allowed : 13.29 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.33 (0.14), residues: 3900 helix: 2.67 (0.10), residues: 2452 sheet: -0.69 (0.31), residues: 268 loop : -0.36 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 327 TYR 0.006 0.001 TYR A1015 PHE 0.011 0.001 PHE A 627 TRP 0.012 0.001 TRP D 579 HIS 0.003 0.001 HIS C1128 Details of bonding type rmsd covalent geometry : bond 0.00306 (30948) covalent geometry : angle 0.49248 (42084) SS BOND : bond 0.00288 ( 8) SS BOND : angle 1.80430 ( 16) hydrogen bonds : bond 0.03445 ( 1892) hydrogen bonds : angle 4.00248 ( 5544) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7663.88 seconds wall clock time: 131 minutes 53.75 seconds (7913.75 seconds total)