Starting phenix.real_space_refine on Tue May 27 21:36:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b93_44367/05_2025/9b93_44367.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b93_44367/05_2025/9b93_44367.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/9b93_44367/05_2025/9b93_44367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b93_44367/05_2025/9b93_44367.map" model { file = "/net/cci-nas-00/data/ceres_data/9b93_44367/05_2025/9b93_44367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b93_44367/05_2025/9b93_44367.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 152 5.16 5 C 19328 2.51 5 N 5272 2.21 5 O 5056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29808 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 7452 Classifications: {'peptide': 984} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PTRANS': 43, 'TRANS': 940} Chain breaks: 10 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 385 Unresolved non-hydrogen angles: 476 Unresolved non-hydrogen dihedrals: 312 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 18, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 269 Restraints were copied for chains: C, B, D Time building chain proxies: 19.44, per 1000 atoms: 0.65 Number of scatterers: 29808 At special positions: 0 Unit cell: (164.772, 163.944, 162.288, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 152 16.00 O 5056 8.00 N 5272 7.00 C 19328 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 37 " distance=2.94 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 37 " distance=2.03 Simple disulfide: pdb=" SG CYS A 993 " - pdb=" SG CYS A1011 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 37 " distance=2.94 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 37 " distance=2.94 Simple disulfide: pdb=" SG CYS D 20 " - pdb=" SG CYS D 37 " distance=2.94 Simple disulfide: pdb=" SG CYS C 35 " - pdb=" SG CYS C 37 " distance=2.03 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 37 " distance=2.03 Simple disulfide: pdb=" SG CYS D 35 " - pdb=" SG CYS D 37 " distance=2.03 Simple disulfide: pdb=" SG CYS C 993 " - pdb=" SG CYS C1011 " distance=2.03 Simple disulfide: pdb=" SG CYS B 993 " - pdb=" SG CYS B1011 " distance=2.03 Simple disulfide: pdb=" SG CYS D 993 " - pdb=" SG CYS D1011 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.60 Conformation dependent library (CDL) restraints added in 4.0 seconds 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7304 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 16 sheets defined 69.0% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.63 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 98 through 108 removed outlier: 3.792A pdb=" N VAL A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 141 Processing helix chain 'A' and resid 141 through 150 Processing helix chain 'A' and resid 160 through 178 removed outlier: 3.757A pdb=" N HIS A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR A 178 " --> pdb=" O GLN A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 201 removed outlier: 4.186A pdb=" N LEU A 200 " --> pdb=" O ASN A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 258 Processing helix chain 'A' and resid 264 through 268 removed outlier: 3.840A pdb=" N THR A 267 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY A 268 " --> pdb=" O GLY A 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 264 through 268' Processing helix chain 'A' and resid 281 through 294 removed outlier: 3.618A pdb=" N THR A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 318 removed outlier: 3.507A pdb=" N THR A 318 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 337 removed outlier: 3.729A pdb=" N GLY A 329 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 removed outlier: 4.425A pdb=" N GLN A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 372 through 386 removed outlier: 3.801A pdb=" N ILE A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.690A pdb=" N ALA A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 435 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 465 Processing helix chain 'A' and resid 471 through 480 Processing helix chain 'A' and resid 502 through 512 removed outlier: 3.781A pdb=" N VAL A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 569 Processing helix chain 'A' and resid 571 through 582 Processing helix chain 'A' and resid 585 through 602 removed outlier: 3.581A pdb=" N LEU A 602 " --> pdb=" O VAL A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 634 removed outlier: 3.582A pdb=" N SER A 633 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 644 Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 669 through 681 Processing helix chain 'A' and resid 689 through 699 Processing helix chain 'A' and resid 700 through 705 Processing helix chain 'A' and resid 767 through 778 Processing helix chain 'A' and resid 778 through 803 Processing helix chain 'A' and resid 811 through 834 Processing helix chain 'A' and resid 852 through 862 removed outlier: 3.643A pdb=" N ASP A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 884 Processing helix chain 'A' and resid 887 through 910 removed outlier: 3.595A pdb=" N MET A 900 " --> pdb=" O CYS A 896 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU A 906 " --> pdb=" O PHE A 902 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU A 907 " --> pdb=" O THR A 903 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N HIS A 908 " --> pdb=" O VAL A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 926 removed outlier: 3.725A pdb=" N SER A 924 " --> pdb=" O ILE A 920 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 925 " --> pdb=" O VAL A 921 " (cutoff:3.500A) 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: 3.808A pdb=" N ILE A 974 " --> pdb=" O PRO A 970 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE A 975 " --> pdb=" O TYR A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 984 removed outlier: 3.597A pdb=" N MET A 983 " --> pdb=" O PRO A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1033 Processing helix chain 'A' and resid 1033 through 1072 removed outlier: 4.953A pdb=" N GLY A1052 " --> pdb=" O GLY A1048 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ASN A1053 " --> pdb=" O LYS A1049 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ARG A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1078 No H-bonds generated for 'chain 'A' and resid 1076 through 1078' Processing helix chain 'A' and resid 1079 through 1088 removed outlier: 4.194A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1143 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: 3.791A pdb=" N VAL B 102 " --> pdb=" O ASP B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 141 Processing helix chain 'B' and resid 141 through 150 Processing helix chain 'B' and resid 160 through 178 removed outlier: 3.757A pdb=" N HIS B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR B 178 " --> pdb=" O GLN B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 201 removed outlier: 4.186A pdb=" N LEU B 200 " --> pdb=" O ASN B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 258 Processing helix chain 'B' and resid 264 through 268 removed outlier: 3.841A pdb=" N THR B 267 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY B 268 " --> pdb=" O GLY B 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 264 through 268' Processing helix chain 'B' and resid 281 through 294 removed outlier: 3.617A pdb=" N THR B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 318 removed outlier: 3.507A pdb=" N THR B 318 " --> pdb=" O THR B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 337 removed outlier: 3.729A pdb=" N GLY B 329 " --> pdb=" O GLY B 325 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 356 removed outlier: 4.423A pdb=" N GLN B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 359 No H-bonds generated for 'chain 'B' and resid 357 through 359' Processing helix chain 'B' and resid 372 through 386 removed outlier: 3.800A pdb=" N ILE B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 405 through 415 removed outlier: 3.690A pdb=" N ALA B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 435 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 465 Processing helix chain 'B' and resid 471 through 480 Processing helix chain 'B' and resid 502 through 512 removed outlier: 3.780A pdb=" N VAL B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 569 Processing helix chain 'B' and resid 571 through 582 Processing helix chain 'B' and resid 585 through 602 removed outlier: 3.581A pdb=" N LEU B 602 " --> pdb=" O VAL B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 634 removed outlier: 3.582A pdb=" N SER B 633 " --> pdb=" O GLU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 644 Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 663 through 668 Processing helix chain 'B' and resid 669 through 681 Processing helix chain 'B' and resid 689 through 699 Processing helix chain 'B' and resid 700 through 705 Processing helix chain 'B' and resid 767 through 778 Processing helix chain 'B' and resid 778 through 803 Processing helix chain 'B' and resid 811 through 834 Processing helix chain 'B' and resid 852 through 862 removed outlier: 3.643A pdb=" N ASP B 862 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 884 Processing helix chain 'B' and resid 887 through 910 removed outlier: 3.596A pdb=" N MET B 900 " --> pdb=" O CYS B 896 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU B 906 " --> pdb=" O PHE B 902 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU B 907 " --> pdb=" O THR B 903 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N HIS B 908 " --> pdb=" O VAL B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 926 removed outlier: 3.726A pdb=" N SER B 924 " --> pdb=" O ILE B 920 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS B 925 " --> pdb=" O VAL B 921 " (cutoff:3.500A) 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: 3.808A pdb=" N ILE B 974 " --> pdb=" O PRO B 970 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE B 975 " --> pdb=" O TYR B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 984 removed outlier: 3.598A pdb=" N MET B 983 " --> pdb=" O PRO B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1033 Processing helix chain 'B' and resid 1033 through 1072 removed outlier: 4.953A pdb=" N GLY B1052 " --> pdb=" O GLY B1048 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ASN B1053 " --> pdb=" O LYS B1049 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR B1063 " --> pdb=" O LYS B1059 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ARG B1064 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1078 No H-bonds generated for 'chain 'B' and resid 1076 through 1078' Processing helix chain 'B' and resid 1079 through 1088 removed outlier: 4.193A pdb=" N SER B1083 " --> pdb=" O PHE B1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1143 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: 3.791A pdb=" N VAL C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 141 Processing helix chain 'C' and resid 141 through 150 Processing helix chain 'C' and resid 160 through 178 removed outlier: 3.758A pdb=" N HIS C 165 " --> pdb=" O GLY C 161 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR C 178 " --> pdb=" O GLN C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 201 removed outlier: 4.187A pdb=" N LEU C 200 " --> pdb=" O ASN C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 258 Processing helix chain 'C' and resid 264 through 268 removed outlier: 3.841A pdb=" N THR C 267 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY C 268 " --> pdb=" O GLY C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 268' Processing helix chain 'C' and resid 281 through 294 removed outlier: 3.618A pdb=" N THR C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 318 removed outlier: 3.506A pdb=" N THR C 318 " --> pdb=" O THR C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 337 removed outlier: 3.729A pdb=" N GLY C 329 " --> pdb=" O GLY C 325 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 356 removed outlier: 4.424A pdb=" N GLN C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 359 No H-bonds generated for 'chain 'C' and resid 357 through 359' Processing helix chain 'C' and resid 372 through 386 removed outlier: 3.801A pdb=" N ILE C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 405 through 415 removed outlier: 3.690A pdb=" N ALA C 409 " --> pdb=" O ARG C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 435 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 465 Processing helix chain 'C' and resid 471 through 480 Processing helix chain 'C' and resid 502 through 512 removed outlier: 3.780A pdb=" N VAL C 506 " --> pdb=" O ASP C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 569 Processing helix chain 'C' and resid 571 through 582 Processing helix chain 'C' and resid 585 through 602 removed outlier: 3.581A pdb=" N LEU C 602 " --> pdb=" O VAL C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 634 removed outlier: 3.582A pdb=" N SER C 633 " --> pdb=" O GLU C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 644 Processing helix chain 'C' and resid 653 through 661 Processing helix chain 'C' and resid 663 through 668 Processing helix chain 'C' and resid 669 through 681 Processing helix chain 'C' and resid 689 through 699 Processing helix chain 'C' and resid 700 through 705 Processing helix chain 'C' and resid 767 through 778 Processing helix chain 'C' and resid 778 through 803 Processing helix chain 'C' and resid 811 through 834 Processing helix chain 'C' and resid 852 through 862 removed outlier: 3.644A pdb=" N ASP C 862 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 884 Processing helix chain 'C' and resid 887 through 910 removed outlier: 3.595A pdb=" N MET C 900 " --> pdb=" O CYS C 896 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU C 906 " --> pdb=" O PHE C 902 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU C 907 " --> pdb=" O THR C 903 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N HIS C 908 " --> pdb=" O VAL C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 926 removed outlier: 3.725A pdb=" N SER C 924 " --> pdb=" O ILE C 920 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS C 925 " --> pdb=" O VAL C 921 " (cutoff:3.500A) 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: 3.807A pdb=" N ILE C 974 " --> pdb=" O PRO C 970 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE C 975 " --> pdb=" O TYR C 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 984 removed outlier: 3.597A pdb=" N MET C 983 " --> pdb=" O PRO C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1033 removed outlier: 3.500A pdb=" N VAL C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1072 removed outlier: 4.954A pdb=" N GLY C1052 " --> pdb=" O GLY C1048 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASN C1053 " --> pdb=" O LYS C1049 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR C1063 " --> pdb=" O LYS C1059 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ARG C1064 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1078 No H-bonds generated for 'chain 'C' and resid 1076 through 1078' Processing helix chain 'C' and resid 1079 through 1088 removed outlier: 4.194A pdb=" N SER C1083 " --> pdb=" O PHE C1079 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1143 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: 3.792A pdb=" N VAL D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 141 Processing helix chain 'D' and resid 141 through 150 Processing helix chain 'D' and resid 160 through 178 removed outlier: 3.757A pdb=" N HIS D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR D 178 " --> pdb=" O GLN D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 201 removed outlier: 4.186A pdb=" N LEU D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 258 Processing helix chain 'D' and resid 264 through 268 removed outlier: 3.840A pdb=" N THR D 267 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY D 268 " --> pdb=" O GLY D 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 264 through 268' Processing helix chain 'D' and resid 281 through 294 removed outlier: 3.618A pdb=" N THR D 286 " --> pdb=" O GLU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 318 removed outlier: 3.507A pdb=" N THR D 318 " --> pdb=" O THR D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 337 removed outlier: 3.729A pdb=" N GLY D 329 " --> pdb=" O GLY D 325 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 356 removed outlier: 4.425A pdb=" N GLN D 348 " --> pdb=" O LEU D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 359 No H-bonds generated for 'chain 'D' and resid 357 through 359' Processing helix chain 'D' and resid 372 through 386 removed outlier: 3.801A pdb=" N ILE D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 403 Processing helix chain 'D' and resid 405 through 415 removed outlier: 3.691A pdb=" N ALA D 409 " --> pdb=" O ARG D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 435 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 465 Processing helix chain 'D' and resid 471 through 480 Processing helix chain 'D' and resid 502 through 512 removed outlier: 3.780A pdb=" N VAL D 506 " --> pdb=" O ASP D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 569 Processing helix chain 'D' and resid 571 through 582 Processing helix chain 'D' and resid 585 through 602 removed outlier: 3.581A pdb=" N LEU D 602 " --> pdb=" O VAL D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 634 removed outlier: 3.581A pdb=" N SER D 633 " --> pdb=" O GLU D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 644 Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 663 through 668 Processing helix chain 'D' and resid 669 through 681 Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 700 through 705 Processing helix chain 'D' and resid 767 through 778 Processing helix chain 'D' and resid 778 through 803 Processing helix chain 'D' and resid 811 through 834 Processing helix chain 'D' and resid 852 through 862 removed outlier: 3.642A pdb=" N ASP D 862 " --> pdb=" O LEU D 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 884 Processing helix chain 'D' and resid 887 through 910 removed outlier: 3.597A pdb=" N MET D 900 " --> pdb=" O CYS D 896 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU D 906 " --> pdb=" O PHE D 902 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU D 907 " --> pdb=" O THR D 903 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N HIS D 908 " --> pdb=" O VAL D 904 " (cutoff:3.500A) Processing helix chain 'D' and resid 916 through 926 removed outlier: 3.725A pdb=" N SER D 924 " --> pdb=" O ILE D 920 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS D 925 " --> pdb=" O VAL D 921 " (cutoff:3.500A) 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: 3.808A pdb=" N ILE D 974 " --> pdb=" O PRO D 970 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE D 975 " --> pdb=" O TYR D 971 " (cutoff:3.500A) Processing helix chain 'D' and resid 979 through 984 removed outlier: 3.597A pdb=" N MET D 983 " --> pdb=" O PRO D 979 " (cutoff:3.500A) Processing helix chain 'D' and resid 1016 through 1033 removed outlier: 3.500A pdb=" N VAL D1020 " --> pdb=" O ALA D1016 " (cutoff:3.500A) Processing helix chain 'D' and resid 1033 through 1072 removed outlier: 4.954A pdb=" N GLY D1052 " --> pdb=" O GLY D1048 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ASN D1053 " --> pdb=" O LYS D1049 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR D1063 " --> pdb=" O LYS D1059 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ARG D1064 " --> pdb=" O ALA D1060 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1078 No H-bonds generated for 'chain 'D' and resid 1076 through 1078' Processing helix chain 'D' and resid 1079 through 1088 removed outlier: 4.194A pdb=" N SER D1083 " --> pdb=" O PHE D1079 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1143 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 78 Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 94 removed outlier: 6.492A pdb=" N LEU A 93 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ALA A 185 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N PHE A 233 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLY A 187 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL A 235 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA A 189 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ILE A 153 " --> pdb=" O MET A 186 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL A 188 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR A 155 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LEU A 299 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU A 275 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL A 301 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU A 277 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N CYS A 298 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N TYR A 364 " --> pdb=" O CYS A 298 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU A 300 " --> pdb=" O TYR A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 989 through 990 removed outlier: 4.162A 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 78 Processing sheet with id=AA7, first strand: chain 'B' and resid 92 through 94 removed outlier: 6.493A pdb=" N LEU B 93 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA B 185 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N PHE B 233 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLY B 187 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL B 235 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA B 189 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ILE B 153 " --> pdb=" O MET B 186 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL B 188 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR B 155 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LEU B 299 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU B 275 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL B 301 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU B 277 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N CYS B 298 " --> pdb=" O THR B 362 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N TYR B 364 " --> pdb=" O CYS B 298 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU B 300 " --> pdb=" O TYR B 364 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 989 through 990 removed outlier: 4.162A 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 78 Processing sheet with id=AB2, first strand: chain 'C' and resid 92 through 94 removed outlier: 6.491A pdb=" N LEU C 93 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA C 185 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N PHE C 233 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLY C 187 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL C 235 " --> pdb=" O GLY C 187 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA C 189 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ILE C 153 " --> pdb=" O MET C 186 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL C 188 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR C 155 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LEU C 299 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU C 275 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL C 301 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU C 277 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N CYS C 298 " --> pdb=" O THR C 362 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N TYR C 364 " --> pdb=" O CYS C 298 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU C 300 " --> pdb=" O TYR C 364 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 989 through 990 removed outlier: 4.161A 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 78 Processing sheet with id=AB6, first strand: chain 'D' and resid 92 through 94 removed outlier: 6.491A pdb=" N LEU D 93 " --> pdb=" O ASP D 236 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA D 185 " --> pdb=" O ALA D 231 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N PHE D 233 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLY D 187 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL D 235 " --> pdb=" O GLY D 187 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA D 189 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ILE D 153 " --> pdb=" O MET D 186 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL D 188 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N THR D 155 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N LEU D 299 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU D 275 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL D 301 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU D 277 " --> pdb=" O VAL D 301 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N CYS D 298 " --> pdb=" O THR D 362 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TYR D 364 " --> pdb=" O CYS D 298 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU D 300 " --> pdb=" O TYR D 364 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 989 through 990 removed outlier: 4.162A pdb=" N GLU D 989 " --> pdb=" O HIS D1002 " (cutoff:3.500A) 1890 hydrogen bonds defined for protein. 5586 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: 10.68 Time building geometry restraints manager: 8.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9672 1.35 - 1.47: 7356 1.47 - 1.59: 13228 1.59 - 1.71: 0 1.71 - 1.83: 232 Bond restraints: 30488 Sorted by residual: bond pdb=" N SER C 469 " pdb=" CA SER C 469 " ideal model delta sigma weight residual 1.457 1.474 -0.016 1.29e-02 6.01e+03 1.58e+00 bond pdb=" N SER A 469 " pdb=" CA SER A 469 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.55e+00 bond pdb=" N SER D 469 " pdb=" CA SER D 469 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.51e+00 bond pdb=" N SER B 469 " pdb=" CA SER B 469 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.45e+00 bond pdb=" N PRO D 809 " pdb=" CA PRO D 809 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.31e-02 5.83e+03 1.15e+00 ... (remaining 30483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 40634 1.27 - 2.53: 585 2.53 - 3.80: 196 3.80 - 5.07: 45 5.07 - 6.34: 16 Bond angle restraints: 41476 Sorted by residual: angle pdb=" C SER A 469 " pdb=" CA SER A 469 " pdb=" CB SER A 469 " ideal model delta sigma weight residual 110.42 115.48 -5.06 1.99e+00 2.53e-01 6.46e+00 angle pdb=" C SER B 469 " pdb=" CA SER B 469 " pdb=" CB SER B 469 " ideal model delta sigma weight residual 110.42 115.46 -5.04 1.99e+00 2.53e-01 6.42e+00 angle pdb=" C SER C 469 " pdb=" CA SER C 469 " pdb=" CB SER C 469 " ideal model delta sigma weight residual 110.42 115.45 -5.03 1.99e+00 2.53e-01 6.38e+00 angle pdb=" C GLY C 263 " pdb=" N VAL C 264 " pdb=" CA VAL C 264 " ideal model delta sigma weight residual 121.97 126.47 -4.50 1.80e+00 3.09e-01 6.26e+00 angle pdb=" C SER D 469 " pdb=" CA SER D 469 " pdb=" CB SER D 469 " ideal model delta sigma weight residual 110.42 115.39 -4.97 1.99e+00 2.53e-01 6.24e+00 ... (remaining 41471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 15407 16.52 - 33.03: 1900 33.03 - 49.55: 481 49.55 - 66.06: 108 66.06 - 82.58: 28 Dihedral angle restraints: 17924 sinusoidal: 6640 harmonic: 11284 Sorted by residual: dihedral pdb=" CB CYS B 993 " pdb=" SG CYS B 993 " pdb=" SG CYS B1011 " pdb=" CB CYS B1011 " ideal model delta sinusoidal sigma weight residual 93.00 145.15 -52.15 1 1.00e+01 1.00e-02 3.71e+01 dihedral pdb=" CB CYS D 993 " pdb=" SG CYS D 993 " pdb=" SG CYS D1011 " pdb=" CB CYS D1011 " ideal model delta sinusoidal sigma weight residual 93.00 145.10 -52.10 1 1.00e+01 1.00e-02 3.70e+01 dihedral pdb=" CB CYS C 993 " pdb=" SG CYS C 993 " pdb=" SG CYS C1011 " pdb=" CB CYS C1011 " ideal model delta sinusoidal sigma weight residual 93.00 145.08 -52.08 1 1.00e+01 1.00e-02 3.70e+01 ... (remaining 17921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 3089 0.025 - 0.050: 1096 0.050 - 0.075: 402 0.075 - 0.100: 150 0.100 - 0.125: 55 Chirality restraints: 4792 Sorted by residual: chirality pdb=" CA ILE C 278 " pdb=" N ILE C 278 " pdb=" C ILE C 278 " pdb=" CB ILE C 278 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CA ILE B 278 " pdb=" N ILE B 278 " pdb=" C ILE B 278 " pdb=" CB ILE B 278 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.89e-01 chirality pdb=" CA ILE D 24 " pdb=" N ILE D 24 " pdb=" C ILE D 24 " pdb=" CB ILE D 24 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.84e-01 ... (remaining 4789 not shown) Planarity restraints: 5228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A1076 " 0.028 5.00e-02 4.00e+02 4.25e-02 2.90e+00 pdb=" N PRO A1077 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A1077 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1077 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B1076 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.87e+00 pdb=" N PRO B1077 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B1077 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B1077 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D1076 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO D1077 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO D1077 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D1077 " 0.023 5.00e-02 4.00e+02 ... (remaining 5225 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1645 2.74 - 3.28: 31266 3.28 - 3.82: 50866 3.82 - 4.36: 57142 4.36 - 4.90: 100695 Nonbonded interactions: 241614 Sorted by model distance: nonbonded pdb=" OG1 THR D 155 " pdb=" OH TYR D 229 " model vdw 2.197 3.040 nonbonded pdb=" OG1 THR B 155 " pdb=" OH TYR B 229 " model vdw 2.197 3.040 nonbonded pdb=" OG1 THR C 155 " pdb=" OH TYR C 229 " model vdw 2.198 3.040 nonbonded pdb=" OG1 THR A 155 " pdb=" OH TYR A 229 " model vdw 2.198 3.040 nonbonded pdb=" O SER C 63 " pdb=" OG1 THR C 67 " model vdw 2.200 3.040 ... (remaining 241609 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.21 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.130 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 66.320 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 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 : 0.011 0.912 30500 Z= 0.530 Angle : 0.509 21.459 41500 Z= 0.259 Chirality : 0.033 0.125 4792 Planarity : 0.004 0.043 5228 Dihedral : 15.662 82.581 10584 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.07 % Allowed : 22.14 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.13), residues: 3848 helix: 2.26 (0.10), residues: 2416 sheet: -0.64 (0.42), residues: 192 loop : -0.43 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1058 HIS 0.006 0.001 HIS C 505 PHE 0.006 0.001 PHE D 933 TYR 0.004 0.001 TYR D1015 ARG 0.003 0.000 ARG A1119 Details of bonding type rmsd hydrogen bonds : bond 0.21743 ( 1890) hydrogen bonds : angle 6.24183 ( 5586) SS BOND : bond 0.52619 ( 12) SS BOND : angle 8.94203 ( 24) covalent geometry : bond 0.00189 (30488) covalent geometry : angle 0.46102 (41476) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 3.313 Fit side-chains REVERT: A 625 ASP cc_start: 0.8949 (m-30) cc_final: 0.8748 (m-30) REVERT: A 988 MET cc_start: 0.8947 (mtm) cc_final: 0.8616 (ptp) REVERT: B 186 MET cc_start: 0.9139 (mmm) cc_final: 0.8816 (mmm) REVERT: B 1034 LEU cc_start: 0.9307 (mp) cc_final: 0.8865 (tt) outliers start: 2 outliers final: 1 residues processed: 126 average time/residue: 0.3626 time to fit residues: 80.4509 Evaluate side-chains 121 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 3.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 936 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 9.9990 chunk 297 optimal weight: 7.9990 chunk 164 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 200 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 chunk 307 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 186 optimal weight: 8.9990 chunk 228 optimal weight: 20.0000 chunk 355 optimal weight: 0.5980 overall best weight: 6.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN A 424 HIS A 584 ASN A 656 GLN A 786 ASN A1014 GLN A1017 ASN B 228 ASN B 424 HIS B 584 ASN B 656 GLN B 786 ASN B1017 ASN C 228 ASN C 424 HIS C 584 ASN C 656 GLN C 786 ASN C1017 ASN D 228 ASN D 424 HIS D 584 ASN D 656 GLN D 786 ASN D1017 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.064407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.047062 restraints weight = 114250.390| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 3.33 r_work: 0.2628 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 30500 Z= 0.347 Angle : 0.647 7.015 41500 Z= 0.335 Chirality : 0.041 0.155 4792 Planarity : 0.005 0.053 5228 Dihedral : 3.905 45.417 4242 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.89 % Allowed : 20.83 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.14), residues: 3848 helix: 2.55 (0.10), residues: 2516 sheet: -0.34 (0.37), residues: 236 loop : -0.53 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 680 HIS 0.006 0.001 HIS B 173 PHE 0.017 0.002 PHE D 627 TYR 0.014 0.001 TYR D1015 ARG 0.005 0.000 ARG C 327 Details of bonding type rmsd hydrogen bonds : bond 0.05566 ( 1890) hydrogen bonds : angle 4.47162 ( 5586) SS BOND : bond 0.00885 ( 12) SS BOND : angle 2.76400 ( 24) covalent geometry : bond 0.00793 (30488) covalent geometry : angle 0.64376 (41476) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 123 time to evaluate : 3.137 Fit side-chains REVERT: A 92 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8855 (ttt-90) REVERT: A 1118 GLU cc_start: 0.9436 (OUTLIER) cc_final: 0.9185 (tm-30) REVERT: B 92 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8137 (ttt180) REVERT: B 926 MET cc_start: 0.9195 (mmt) cc_final: 0.8860 (mmt) REVERT: B 1118 GLU cc_start: 0.9439 (OUTLIER) cc_final: 0.9164 (tm-30) REVERT: C 92 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.7883 (ttt-90) REVERT: C 509 MET cc_start: 0.8587 (mmp) cc_final: 0.8340 (mmp) REVERT: C 926 MET cc_start: 0.9198 (mmt) cc_final: 0.8817 (mmt) REVERT: C 1118 GLU cc_start: 0.9448 (OUTLIER) cc_final: 0.9127 (pp20) REVERT: D 92 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.8418 (ttt-90) REVERT: D 1146 GLU cc_start: 0.9125 (OUTLIER) cc_final: 0.8570 (mp0) outliers start: 84 outliers final: 41 residues processed: 191 average time/residue: 0.4025 time to fit residues: 126.1515 Evaluate side-chains 166 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 117 time to evaluate : 3.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 927 MET Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 1017 ASN Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1146 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1017 ASN Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1118 GLU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 787 VAL Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1017 ASN Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1118 GLU Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1146 GLU Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 787 VAL Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 1017 ASN Chi-restraints excluded: chain D residue 1146 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 220 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 252 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 235 optimal weight: 1.9990 chunk 159 optimal weight: 8.9990 chunk 342 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 265 optimal weight: 10.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1014 GLN C1014 GLN D1014 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.066403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.049049 restraints weight = 112722.216| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 3.35 r_work: 0.2691 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30500 Z= 0.123 Angle : 0.479 6.302 41500 Z= 0.250 Chirality : 0.035 0.127 4792 Planarity : 0.004 0.045 5228 Dihedral : 3.740 21.840 4240 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.58 % Allowed : 20.66 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.14), residues: 3848 helix: 2.79 (0.10), residues: 2516 sheet: -0.50 (0.36), residues: 236 loop : -0.53 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1058 HIS 0.004 0.001 HIS C 424 PHE 0.013 0.001 PHE C 627 TYR 0.011 0.001 TYR C1015 ARG 0.005 0.000 ARG C 92 Details of bonding type rmsd hydrogen bonds : bond 0.04500 ( 1890) hydrogen bonds : angle 4.03115 ( 5586) SS BOND : bond 0.01062 ( 12) SS BOND : angle 2.22043 ( 24) covalent geometry : bond 0.00262 (30488) covalent geometry : angle 0.47648 (41476) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 130 time to evaluate : 3.074 Fit side-chains REVERT: A 92 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8172 (ttt-90) REVERT: A 284 MET cc_start: 0.9168 (mmm) cc_final: 0.8829 (mmm) REVERT: A 625 ASP cc_start: 0.9049 (m-30) cc_final: 0.8837 (m-30) REVERT: B 92 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8705 (ttt-90) REVERT: B 509 MET cc_start: 0.8508 (mmp) cc_final: 0.8302 (mmp) REVERT: B 926 MET cc_start: 0.9123 (mmt) cc_final: 0.8855 (mmt) REVERT: B 936 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8554 (m-80) REVERT: C 92 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.7914 (ttt-90) REVERT: C 926 MET cc_start: 0.9089 (mmt) cc_final: 0.8834 (mmt) REVERT: D 92 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8683 (ttt-90) REVERT: D 1118 GLU cc_start: 0.9280 (OUTLIER) cc_final: 0.8998 (pp20) outliers start: 75 outliers final: 34 residues processed: 189 average time/residue: 0.3754 time to fit residues: 119.9390 Evaluate side-chains 166 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 126 time to evaluate : 3.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1165 ILE Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 936 PHE Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1118 GLU Chi-restraints excluded: chain D residue 1165 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 325 optimal weight: 20.0000 chunk 164 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 253 optimal weight: 0.7980 chunk 187 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 224 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1014 GLN B1017 ASN C1017 ASN D1014 GLN D1017 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.066144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.048857 restraints weight = 112905.709| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.35 r_work: 0.2685 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30500 Z= 0.153 Angle : 0.479 6.339 41500 Z= 0.248 Chirality : 0.036 0.125 4792 Planarity : 0.004 0.046 5228 Dihedral : 3.667 22.475 4240 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.96 % Allowed : 20.59 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.14), residues: 3848 helix: 2.86 (0.10), residues: 2520 sheet: -0.58 (0.36), residues: 236 loop : -0.53 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 680 HIS 0.005 0.001 HIS D 424 PHE 0.016 0.001 PHE B 627 TYR 0.010 0.001 TYR C1015 ARG 0.005 0.000 ARG A 327 Details of bonding type rmsd hydrogen bonds : bond 0.04166 ( 1890) hydrogen bonds : angle 3.90343 ( 5586) SS BOND : bond 0.00693 ( 12) SS BOND : angle 1.72899 ( 24) covalent geometry : bond 0.00344 (30488) covalent geometry : angle 0.47761 (41476) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 129 time to evaluate : 3.159 Fit side-chains REVERT: A 92 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8215 (ttt-90) REVERT: A 284 MET cc_start: 0.9114 (mmm) cc_final: 0.8845 (mmm) REVERT: A 509 MET cc_start: 0.8582 (mmp) cc_final: 0.8350 (mmp) REVERT: A 625 ASP cc_start: 0.9070 (m-30) cc_final: 0.8834 (m-30) REVERT: A 784 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8361 (ttm) REVERT: B 92 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8306 (ttt-90) REVERT: B 872 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8764 (mm) REVERT: B 926 MET cc_start: 0.9131 (mmt) cc_final: 0.8882 (mmt) REVERT: B 1037 ASN cc_start: 0.9370 (m-40) cc_final: 0.9123 (m-40) REVERT: B 1118 GLU cc_start: 0.9373 (OUTLIER) cc_final: 0.9102 (tm-30) REVERT: B 1156 ASP cc_start: 0.9166 (m-30) cc_final: 0.8958 (m-30) REVERT: C 92 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.7896 (ttt-90) REVERT: C 872 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8886 (mm) REVERT: C 926 MET cc_start: 0.9123 (mmt) cc_final: 0.8886 (mmt) REVERT: C 1118 GLU cc_start: 0.9364 (OUTLIER) cc_final: 0.9062 (pp20) REVERT: C 1156 ASP cc_start: 0.9209 (m-30) cc_final: 0.8864 (m-30) REVERT: D 92 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8699 (ttt-90) REVERT: D 284 MET cc_start: 0.9125 (mmm) cc_final: 0.8770 (mmm) REVERT: D 784 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8400 (ttm) REVERT: D 1118 GLU cc_start: 0.9304 (OUTLIER) cc_final: 0.9025 (pp20) outliers start: 86 outliers final: 46 residues processed: 200 average time/residue: 0.3556 time to fit residues: 121.8226 Evaluate side-chains 181 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 124 time to evaluate : 3.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1146 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1017 ASN Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1118 GLU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1017 ASN Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1118 GLU Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1146 GLU Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1017 ASN Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1118 GLU Chi-restraints excluded: chain D residue 1165 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 76 optimal weight: 3.9990 chunk 212 optimal weight: 0.9990 chunk 250 optimal weight: 0.7980 chunk 351 optimal weight: 0.8980 chunk 357 optimal weight: 6.9990 chunk 300 optimal weight: 8.9990 chunk 144 optimal weight: 0.8980 chunk 383 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 203 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1014 GLN ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1014 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.067147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.049892 restraints weight = 111430.584| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.34 r_work: 0.2720 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 30500 Z= 0.102 Angle : 0.449 6.456 41500 Z= 0.233 Chirality : 0.035 0.126 4792 Planarity : 0.003 0.044 5228 Dihedral : 3.617 20.954 4240 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.44 % Allowed : 21.25 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.14), residues: 3848 helix: 2.90 (0.10), residues: 2532 sheet: -0.66 (0.36), residues: 236 loop : -0.46 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1058 HIS 0.003 0.001 HIS C 424 PHE 0.013 0.001 PHE B 423 TYR 0.009 0.001 TYR D1015 ARG 0.006 0.000 ARG D 327 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 1890) hydrogen bonds : angle 3.78089 ( 5586) SS BOND : bond 0.00675 ( 12) SS BOND : angle 1.62474 ( 24) covalent geometry : bond 0.00213 (30488) covalent geometry : angle 0.44788 (41476) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 132 time to evaluate : 3.100 Fit side-chains REVERT: A 92 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8450 (ttt-90) REVERT: A 284 MET cc_start: 0.9050 (mmm) cc_final: 0.8834 (mmm) REVERT: A 625 ASP cc_start: 0.9063 (m-30) cc_final: 0.8805 (m-30) REVERT: A 784 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8294 (ttm) REVERT: A 1156 ASP cc_start: 0.9212 (m-30) cc_final: 0.8837 (m-30) REVERT: B 92 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8387 (ttt-90) REVERT: B 509 MET cc_start: 0.8483 (mmp) cc_final: 0.8276 (mmp) REVERT: B 926 MET cc_start: 0.9075 (mmt) cc_final: 0.8873 (mmt) REVERT: B 936 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.8507 (m-80) REVERT: B 1118 GLU cc_start: 0.9335 (OUTLIER) cc_final: 0.9065 (tm-30) REVERT: C 92 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.7931 (ttt-90) REVERT: C 1156 ASP cc_start: 0.9227 (m-30) cc_final: 0.8856 (m-30) REVERT: D 284 MET cc_start: 0.9089 (mmm) cc_final: 0.8851 (mmm) REVERT: D 784 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8328 (ttm) REVERT: D 1118 GLU cc_start: 0.9280 (OUTLIER) cc_final: 0.8998 (pp20) REVERT: D 1146 GLU cc_start: 0.9313 (OUTLIER) cc_final: 0.9104 (mm-30) outliers start: 71 outliers final: 40 residues processed: 185 average time/residue: 0.3481 time to fit residues: 111.7038 Evaluate side-chains 175 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 126 time to evaluate : 3.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1146 GLU Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1118 GLU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 983 MET Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1146 GLU Chi-restraints excluded: chain C residue 1165 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1118 GLU Chi-restraints excluded: chain D residue 1146 GLU Chi-restraints excluded: chain D residue 1165 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 80 optimal weight: 0.0980 chunk 11 optimal weight: 5.9990 chunk 374 optimal weight: 0.9990 chunk 170 optimal weight: 5.9990 chunk 211 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 341 optimal weight: 6.9990 chunk 226 optimal weight: 0.0770 chunk 296 optimal weight: 30.0000 chunk 156 optimal weight: 9.9990 chunk 252 optimal weight: 7.9990 overall best weight: 2.6344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1014 GLN ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1017 ASN C1161 GLN D1014 GLN D1017 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.066317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.048854 restraints weight = 111795.671| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 3.44 r_work: 0.2680 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 30500 Z= 0.162 Angle : 0.479 6.867 41500 Z= 0.246 Chirality : 0.036 0.123 4792 Planarity : 0.004 0.046 5228 Dihedral : 3.579 21.777 4240 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.51 % Allowed : 21.21 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.14), residues: 3848 helix: 2.94 (0.10), residues: 2528 sheet: -0.62 (0.37), residues: 236 loop : -0.46 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1018 HIS 0.004 0.001 HIS D 424 PHE 0.015 0.001 PHE A 627 TYR 0.010 0.001 TYR C1015 ARG 0.008 0.000 ARG D 92 Details of bonding type rmsd hydrogen bonds : bond 0.03919 ( 1890) hydrogen bonds : angle 3.79345 ( 5586) SS BOND : bond 0.00552 ( 12) SS BOND : angle 1.44097 ( 24) covalent geometry : bond 0.00370 (30488) covalent geometry : angle 0.47779 (41476) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 124 time to evaluate : 3.606 Fit side-chains REVERT: A 92 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8260 (ttt-90) REVERT: A 509 MET cc_start: 0.8543 (mmp) cc_final: 0.8334 (mmp) REVERT: A 625 ASP cc_start: 0.9164 (m-30) cc_final: 0.8858 (m-30) REVERT: A 784 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8042 (ttm) REVERT: A 988 MET cc_start: 0.8685 (mtm) cc_final: 0.8456 (ptp) REVERT: A 1118 GLU cc_start: 0.9338 (OUTLIER) cc_final: 0.9068 (pp20) REVERT: B 509 MET cc_start: 0.8502 (mmp) cc_final: 0.8233 (mmp) REVERT: B 926 MET cc_start: 0.8941 (mmt) cc_final: 0.8691 (mmt) REVERT: B 1118 GLU cc_start: 0.9425 (OUTLIER) cc_final: 0.9106 (tm-30) REVERT: C 581 MET cc_start: 0.9181 (mmm) cc_final: 0.8976 (mmp) REVERT: C 1118 GLU cc_start: 0.9418 (OUTLIER) cc_final: 0.9090 (pp20) REVERT: C 1156 ASP cc_start: 0.9268 (m-30) cc_final: 0.8875 (m-30) REVERT: D 284 MET cc_start: 0.9152 (mmm) cc_final: 0.8928 (mmm) REVERT: D 509 MET cc_start: 0.8487 (mmp) cc_final: 0.8244 (mmp) REVERT: D 784 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8119 (ttm) REVERT: D 1118 GLU cc_start: 0.9351 (OUTLIER) cc_final: 0.9051 (pp20) outliers start: 73 outliers final: 50 residues processed: 185 average time/residue: 0.3505 time to fit residues: 113.5080 Evaluate side-chains 179 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 122 time to evaluate : 3.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1146 GLU Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1118 GLU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1017 ASN Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain C residue 1118 GLU Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1146 GLU Chi-restraints excluded: chain C residue 1165 ILE Chi-restraints excluded: chain D residue 622 MET Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1014 GLN Chi-restraints excluded: chain D residue 1017 ASN Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1118 GLU Chi-restraints excluded: chain D residue 1165 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 360 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 385 optimal weight: 7.9990 chunk 159 optimal weight: 0.2980 chunk 17 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 239 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1014 GLN ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1017 ASN D1014 GLN D1017 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.065844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.048344 restraints weight = 111800.220| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 3.43 r_work: 0.2668 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 30500 Z= 0.199 Angle : 0.502 6.629 41500 Z= 0.257 Chirality : 0.037 0.185 4792 Planarity : 0.004 0.047 5228 Dihedral : 3.602 21.714 4240 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.06 % Allowed : 20.66 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.14), residues: 3848 helix: 2.97 (0.10), residues: 2516 sheet: -0.60 (0.37), residues: 236 loop : -0.53 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 680 HIS 0.003 0.001 HIS A1128 PHE 0.015 0.001 PHE B 627 TYR 0.010 0.001 TYR B1015 ARG 0.006 0.000 ARG D 92 Details of bonding type rmsd hydrogen bonds : bond 0.04020 ( 1890) hydrogen bonds : angle 3.84121 ( 5586) SS BOND : bond 0.00540 ( 12) SS BOND : angle 1.38539 ( 24) covalent geometry : bond 0.00454 (30488) covalent geometry : angle 0.50109 (41476) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 124 time to evaluate : 3.231 Fit side-chains revert: symmetry clash REVERT: A 509 MET cc_start: 0.8516 (mmp) cc_final: 0.8252 (mmp) REVERT: A 625 ASP cc_start: 0.9170 (m-30) cc_final: 0.8845 (m-30) REVERT: A 784 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8030 (ttm) REVERT: B 92 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.7970 (ttt-90) REVERT: B 926 MET cc_start: 0.8970 (mmt) cc_final: 0.8703 (mmt) REVERT: B 1118 GLU cc_start: 0.9451 (OUTLIER) cc_final: 0.9138 (tm-30) REVERT: C 581 MET cc_start: 0.9209 (mmm) cc_final: 0.9008 (mmp) REVERT: C 1118 GLU cc_start: 0.9434 (OUTLIER) cc_final: 0.9104 (pp20) REVERT: D 284 MET cc_start: 0.9134 (mmm) cc_final: 0.8932 (mmm) REVERT: D 509 MET cc_start: 0.8518 (mmp) cc_final: 0.8248 (mmp) REVERT: D 784 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8103 (ttm) REVERT: D 1118 GLU cc_start: 0.9363 (OUTLIER) cc_final: 0.9060 (pp20) outliers start: 89 outliers final: 55 residues processed: 196 average time/residue: 0.3562 time to fit residues: 120.6871 Evaluate side-chains 183 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 122 time to evaluate : 3.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1146 GLU Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1118 GLU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 787 VAL Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 983 MET Chi-restraints excluded: chain C residue 1014 GLN Chi-restraints excluded: chain C residue 1017 ASN Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1118 GLU Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1165 ILE Chi-restraints excluded: chain D residue 622 MET Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1014 GLN Chi-restraints excluded: chain D residue 1017 ASN Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1118 GLU Chi-restraints excluded: chain D residue 1165 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 328 optimal weight: 6.9990 chunk 253 optimal weight: 1.9990 chunk 228 optimal weight: 5.9990 chunk 342 optimal weight: 2.9990 chunk 309 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 chunk 205 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 381 optimal weight: 2.9990 chunk 275 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 990 HIS ** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1014 GLN C1017 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.066253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.048843 restraints weight = 111991.261| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.42 r_work: 0.2680 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 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 : 0.003 0.035 30500 Z= 0.148 Angle : 0.478 8.174 41500 Z= 0.245 Chirality : 0.036 0.135 4792 Planarity : 0.003 0.046 5228 Dihedral : 3.610 21.343 4240 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.62 % Allowed : 21.07 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.14), residues: 3848 helix: 2.99 (0.10), residues: 2516 sheet: -0.60 (0.37), residues: 236 loop : -0.50 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 680 HIS 0.003 0.001 HIS C 424 PHE 0.014 0.001 PHE A 627 TYR 0.009 0.001 TYR C1015 ARG 0.005 0.000 ARG D 92 Details of bonding type rmsd hydrogen bonds : bond 0.03888 ( 1890) hydrogen bonds : angle 3.78696 ( 5586) SS BOND : bond 0.00519 ( 12) SS BOND : angle 1.37997 ( 24) covalent geometry : bond 0.00336 (30488) covalent geometry : angle 0.47657 (41476) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 125 time to evaluate : 3.341 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8298 (ttt-90) REVERT: A 509 MET cc_start: 0.8523 (mmp) cc_final: 0.8235 (mmp) REVERT: A 625 ASP cc_start: 0.9159 (m-30) cc_final: 0.8859 (m-30) REVERT: A 784 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8000 (ttm) REVERT: B 92 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.7998 (ttt-90) REVERT: B 926 MET cc_start: 0.8962 (mmt) cc_final: 0.8710 (mmt) REVERT: B 1118 GLU cc_start: 0.9434 (OUTLIER) cc_final: 0.9117 (tm-30) REVERT: C 1118 GLU cc_start: 0.9423 (OUTLIER) cc_final: 0.9095 (pp20) REVERT: C 1156 ASP cc_start: 0.9286 (m-30) cc_final: 0.8864 (m-30) REVERT: D 355 MET cc_start: 0.9440 (mmm) cc_final: 0.9211 (mmm) REVERT: D 509 MET cc_start: 0.8535 (mmp) cc_final: 0.8246 (mmp) REVERT: D 784 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8073 (ttm) REVERT: D 1118 GLU cc_start: 0.9356 (OUTLIER) cc_final: 0.9053 (pp20) outliers start: 76 outliers final: 52 residues processed: 188 average time/residue: 0.3528 time to fit residues: 114.8221 Evaluate side-chains 182 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 123 time to evaluate : 3.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1146 GLU Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 983 MET Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1118 GLU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1014 GLN Chi-restraints excluded: chain C residue 1017 ASN Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain C residue 1118 GLU Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1146 GLU Chi-restraints excluded: chain C residue 1165 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 622 MET Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 983 MET Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1118 GLU Chi-restraints excluded: chain D residue 1165 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 177 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 153 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 269 optimal weight: 4.9990 chunk 263 optimal weight: 1.9990 chunk 355 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 312 optimal weight: 8.9990 chunk 342 optimal weight: 5.9990 chunk 364 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1161 GLN ** B1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1017 ASN D1014 GLN D1017 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.065937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.048526 restraints weight = 111370.872| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 3.42 r_work: 0.2672 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30500 Z= 0.177 Angle : 0.494 10.204 41500 Z= 0.253 Chirality : 0.036 0.135 4792 Planarity : 0.004 0.047 5228 Dihedral : 3.599 21.283 4240 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.41 % Allowed : 21.49 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.14), residues: 3848 helix: 3.01 (0.10), residues: 2508 sheet: -0.60 (0.37), residues: 236 loop : -0.51 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 579 HIS 0.008 0.001 HIS B 505 PHE 0.014 0.001 PHE A 627 TYR 0.016 0.001 TYR C1015 ARG 0.005 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.03934 ( 1890) hydrogen bonds : angle 3.81224 ( 5586) SS BOND : bond 0.00485 ( 12) SS BOND : angle 1.33434 ( 24) covalent geometry : bond 0.00403 (30488) covalent geometry : angle 0.49314 (41476) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 120 time to evaluate : 3.535 Fit side-chains REVERT: A 92 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8276 (ttt-90) REVERT: A 509 MET cc_start: 0.8559 (mmp) cc_final: 0.8273 (mmp) REVERT: A 625 ASP cc_start: 0.9177 (m-30) cc_final: 0.8887 (m-30) REVERT: A 784 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8008 (ttm) REVERT: B 92 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.7949 (ttt-90) REVERT: B 643 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9391 (mm) REVERT: B 926 MET cc_start: 0.8979 (mmt) cc_final: 0.8726 (mmt) REVERT: B 1118 GLU cc_start: 0.9446 (OUTLIER) cc_final: 0.9132 (tm-30) REVERT: C 92 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.7733 (ttt180) REVERT: C 1118 GLU cc_start: 0.9434 (OUTLIER) cc_final: 0.9105 (pp20) REVERT: D 355 MET cc_start: 0.9453 (mmm) cc_final: 0.9224 (mmm) REVERT: D 784 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8082 (ttm) REVERT: D 1118 GLU cc_start: 0.9368 (OUTLIER) cc_final: 0.9066 (pp20) outliers start: 70 outliers final: 52 residues processed: 176 average time/residue: 0.3779 time to fit residues: 117.0923 Evaluate side-chains 182 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 121 time to evaluate : 3.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1146 GLU Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1118 GLU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 787 VAL Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 983 MET Chi-restraints excluded: chain C residue 1014 GLN Chi-restraints excluded: chain C residue 1017 ASN Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1118 GLU Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1165 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 622 MET Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1014 GLN Chi-restraints excluded: chain D residue 1017 ASN Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1118 GLU Chi-restraints excluded: chain D residue 1165 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 225 optimal weight: 40.0000 chunk 361 optimal weight: 1.9990 chunk 336 optimal weight: 5.9990 chunk 299 optimal weight: 10.0000 chunk 190 optimal weight: 0.9990 chunk 256 optimal weight: 0.6980 chunk 107 optimal weight: 9.9990 chunk 345 optimal weight: 8.9990 chunk 378 optimal weight: 0.9980 chunk 352 optimal weight: 8.9990 chunk 266 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1017 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.066295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.048907 restraints weight = 111725.668| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 3.42 r_work: 0.2683 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30500 Z= 0.141 Angle : 0.482 10.240 41500 Z= 0.246 Chirality : 0.036 0.126 4792 Planarity : 0.003 0.046 5228 Dihedral : 3.601 20.809 4240 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.07 % Allowed : 21.87 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.14), residues: 3848 helix: 3.00 (0.10), residues: 2520 sheet: -0.60 (0.37), residues: 236 loop : -0.47 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1058 HIS 0.003 0.001 HIS C 424 PHE 0.013 0.001 PHE A 627 TYR 0.009 0.001 TYR B1015 ARG 0.005 0.000 ARG D 92 Details of bonding type rmsd hydrogen bonds : bond 0.03823 ( 1890) hydrogen bonds : angle 3.77319 ( 5586) SS BOND : bond 0.00490 ( 12) SS BOND : angle 1.34579 ( 24) covalent geometry : bond 0.00318 (30488) covalent geometry : angle 0.48139 (41476) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 123 time to evaluate : 3.796 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8308 (ttt-90) REVERT: A 509 MET cc_start: 0.8570 (mmp) cc_final: 0.8294 (mmp) REVERT: A 625 ASP cc_start: 0.9168 (m-30) cc_final: 0.8872 (m-30) REVERT: A 784 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8031 (ttm) REVERT: B 92 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8024 (ttt-90) REVERT: B 643 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9401 (mm) REVERT: B 926 MET cc_start: 0.8989 (mmt) cc_final: 0.8742 (mmt) REVERT: B 1118 GLU cc_start: 0.9432 (OUTLIER) cc_final: 0.9118 (tm-30) REVERT: C 1118 GLU cc_start: 0.9420 (OUTLIER) cc_final: 0.9094 (pp20) REVERT: D 355 MET cc_start: 0.9467 (mmm) cc_final: 0.9232 (mmm) REVERT: D 784 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8107 (ttm) REVERT: D 1118 GLU cc_start: 0.9363 (OUTLIER) cc_final: 0.9062 (pp20) outliers start: 60 outliers final: 49 residues processed: 175 average time/residue: 0.3381 time to fit residues: 104.5825 Evaluate side-chains 179 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 122 time to evaluate : 3.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1146 GLU Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1118 GLU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1118 GLU Chi-restraints excluded: chain C residue 1165 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 622 MET Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain D residue 787 VAL Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1017 ASN Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1118 GLU Chi-restraints excluded: chain D residue 1165 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 6 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 198 optimal weight: 40.0000 chunk 24 optimal weight: 2.9990 chunk 338 optimal weight: 3.9990 chunk 241 optimal weight: 10.0000 chunk 379 optimal weight: 0.7980 chunk 50 optimal weight: 10.0000 chunk 252 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1017 ASN D1014 GLN D1017 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.065660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.048212 restraints weight = 111811.650| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 3.43 r_work: 0.2665 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30500 Z= 0.196 Angle : 0.507 9.772 41500 Z= 0.259 Chirality : 0.037 0.133 4792 Planarity : 0.004 0.047 5228 Dihedral : 3.602 21.217 4240 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.44 % Allowed : 21.63 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.14), residues: 3848 helix: 3.02 (0.10), residues: 2508 sheet: -0.60 (0.37), residues: 236 loop : -0.47 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C1018 HIS 0.007 0.001 HIS D 505 PHE 0.015 0.001 PHE B 627 TYR 0.018 0.001 TYR D1015 ARG 0.005 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.03969 ( 1890) hydrogen bonds : angle 3.82376 ( 5586) SS BOND : bond 0.00465 ( 12) SS BOND : angle 1.29344 ( 24) covalent geometry : bond 0.00448 (30488) covalent geometry : angle 0.50658 (41476) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13092.86 seconds wall clock time: 227 minutes 32.10 seconds (13652.10 seconds total)