Starting phenix.real_space_refine on Mon Aug 25 18:26:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b93_44367/08_2025/9b93_44367.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b93_44367/08_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_44367/08_2025/9b93_44367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b93_44367/08_2025/9b93_44367.map" model { file = "/net/cci-nas-00/data/ceres_data/9b93_44367/08_2025/9b93_44367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b93_44367/08_2025/9b93_44367.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'GLU:plan': 17, 'PHE:plan': 5, 'GLN:plan1': 5, 'ARG:plan': 14, 'ASP:plan': 18, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 269 Restraints were copied for chains: B, C, D Time building chain proxies: 9.05, per 1000 atoms: 0.30 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 B 20 " - pdb=" SG CYS B 37 " distance=2.94 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 37 " distance=2.94 Simple disulfide: pdb=" SG CYS D 20 " - pdb=" SG CYS D 37 " distance=2.94 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 37 " distance=2.03 Simple disulfide: pdb=" SG CYS C 35 " - pdb=" SG CYS C 37 " distance=2.03 Simple disulfide: pdb=" SG CYS D 35 " - pdb=" SG CYS D 37 " distance=2.03 Simple disulfide: pdb=" SG CYS B 993 " - pdb=" SG CYS B1011 " distance=2.03 Simple disulfide: pdb=" SG CYS C 993 " - pdb=" SG CYS C1011 " distance=2.03 Simple disulfide: pdb=" SG CYS D 993 " - pdb=" SG CYS D1011 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.42 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: 8.41 Time building geometry restraints manager: 3.85 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.270 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: 0.720 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 33.730 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:1.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.130 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (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 ARG 0.003 0.000 ARG A1119 TYR 0.004 0.001 TYR D1015 PHE 0.006 0.001 PHE D 933 TRP 0.010 0.001 TRP A1058 HIS 0.006 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00189 (30488) covalent geometry : angle 0.46102 (41476) SS BOND : bond 0.52619 ( 12) SS BOND : angle 8.94203 ( 24) hydrogen bonds : bond 0.21743 ( 1890) hydrogen bonds : angle 6.24183 ( 5586) *********************** 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 : 0.822 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: 0.1687 time to fit residues: 37.3061 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 : 0.901 ------------------------------------------------------------------------------- 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 197 optimal weight: 30.0000 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.0050 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.0170 chunk 183 optimal weight: 5.9990 overall best weight: 1.3634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN A 584 ASN A 656 GLN A 786 ASN A1017 ASN B 228 ASN B 584 ASN B 656 GLN B 786 ASN B1017 ASN C 228 ASN C 584 ASN C 656 GLN C 786 ASN C1017 ASN D 228 ASN D 584 ASN D 656 GLN D 786 ASN D1017 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.066795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.049571 restraints weight = 111810.931| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 3.34 r_work: 0.2706 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30500 Z= 0.137 Angle : 0.502 7.316 41500 Z= 0.266 Chirality : 0.036 0.128 4792 Planarity : 0.004 0.043 5228 Dihedral : 3.669 45.645 4242 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.76 % Allowed : 20.70 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.47 (0.14), residues: 3848 helix: 2.73 (0.10), residues: 2512 sheet: -0.90 (0.38), residues: 216 loop : -0.43 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 92 TYR 0.007 0.001 TYR D1015 PHE 0.013 0.001 PHE D 627 TRP 0.012 0.001 TRP D 579 HIS 0.003 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00280 (30488) covalent geometry : angle 0.49427 (41476) SS BOND : bond 0.01382 ( 12) SS BOND : angle 3.56717 ( 24) hydrogen bonds : bond 0.05246 ( 1890) hydrogen bonds : angle 4.26747 ( 5586) *********************** 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 186 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 135 time to evaluate : 0.882 Fit side-chains REVERT: A 92 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.8176 (ttt-90) REVERT: A 625 ASP cc_start: 0.8983 (m-30) cc_final: 0.8740 (m-30) REVERT: B 92 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8713 (ttt-90) REVERT: B 186 MET cc_start: 0.9012 (mmm) cc_final: 0.8700 (mmm) REVERT: B 926 MET cc_start: 0.9029 (mmt) cc_final: 0.8767 (mmt) REVERT: B 936 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8574 (m-80) REVERT: B 1156 ASP cc_start: 0.9081 (m-30) cc_final: 0.8772 (m-30) REVERT: C 92 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.7924 (ttt-90) REVERT: C 926 MET cc_start: 0.9033 (mmt) cc_final: 0.8677 (mmt) REVERT: C 1156 ASP cc_start: 0.9138 (m-30) cc_final: 0.8845 (m-30) REVERT: D 92 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8705 (ttt-90) REVERT: D 625 ASP cc_start: 0.9000 (m-30) cc_final: 0.8770 (m-30) outliers start: 51 outliers final: 19 residues processed: 169 average time/residue: 0.1814 time to fit residues: 49.6099 Evaluate side-chains 148 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 1017 ASN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 599 MET 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 1017 ASN Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 1017 ASN Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 936 PHE Chi-restraints excluded: chain D residue 1017 ASN Chi-restraints excluded: chain D residue 1032 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 217 optimal weight: 9.9990 chunk 368 optimal weight: 7.9990 chunk 360 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 371 optimal weight: 6.9990 chunk 241 optimal weight: 10.0000 chunk 361 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 374 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1017 ASN B1017 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.066737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.049541 restraints weight = 112846.668| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.34 r_work: 0.2702 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30500 Z= 0.141 Angle : 0.474 6.314 41500 Z= 0.247 Chirality : 0.035 0.126 4792 Planarity : 0.004 0.044 5228 Dihedral : 3.655 45.527 4242 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.44 % Allowed : 20.14 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.59 (0.14), residues: 3848 helix: 2.86 (0.10), residues: 2516 sheet: -0.90 (0.38), residues: 216 loop : -0.48 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 92 TYR 0.010 0.001 TYR D1015 PHE 0.014 0.001 PHE D 627 TRP 0.009 0.001 TRP C 772 HIS 0.005 0.001 HIS B 447 Details of bonding type rmsd covalent geometry : bond 0.00312 (30488) covalent geometry : angle 0.47121 (41476) SS BOND : bond 0.01143 ( 12) SS BOND : angle 2.34631 ( 24) hydrogen bonds : bond 0.04572 ( 1890) hydrogen bonds : angle 4.00786 ( 5586) *********************** 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 206 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 135 time to evaluate : 1.135 Fit side-chains REVERT: A 92 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8155 (ttt-90) REVERT: A 625 ASP cc_start: 0.9045 (m-30) cc_final: 0.8778 (m-30) REVERT: A 1017 ASN cc_start: 0.7879 (OUTLIER) cc_final: 0.7618 (t0) REVERT: A 1118 GLU cc_start: 0.9317 (OUTLIER) cc_final: 0.9081 (tm-30) REVERT: B 92 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8328 (ttt-90) REVERT: B 186 MET cc_start: 0.9028 (mmm) cc_final: 0.8699 (mmm) REVERT: B 643 LEU cc_start: 0.9672 (OUTLIER) cc_final: 0.9469 (mm) REVERT: B 926 MET cc_start: 0.9070 (mmt) cc_final: 0.8848 (mmt) REVERT: B 936 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.8547 (m-80) REVERT: B 1017 ASN cc_start: 0.7908 (OUTLIER) cc_final: 0.7538 (t0) REVERT: B 1037 ASN cc_start: 0.9377 (m-40) cc_final: 0.9114 (m-40) REVERT: B 1118 GLU cc_start: 0.9359 (OUTLIER) cc_final: 0.9086 (tm-30) REVERT: B 1156 ASP cc_start: 0.9106 (m-30) cc_final: 0.8771 (m-30) REVERT: C 92 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.7930 (ttt-90) REVERT: C 509 MET cc_start: 0.8497 (mmp) cc_final: 0.8295 (mmp) REVERT: C 1118 GLU cc_start: 0.9343 (OUTLIER) cc_final: 0.9030 (pp20) REVERT: C 1156 ASP cc_start: 0.9185 (m-30) cc_final: 0.8863 (m-30) REVERT: D 92 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8672 (ttt-90) REVERT: D 625 ASP cc_start: 0.9082 (m-30) cc_final: 0.8841 (m-30) outliers start: 71 outliers final: 32 residues processed: 189 average time/residue: 0.1712 time to fit residues: 55.5005 Evaluate side-chains 172 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 1017 ASN Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1118 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 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 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 B residue 1125 GLU Chi-restraints excluded: chain B residue 1165 ILE 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 709 THR 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 1118 GLU Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 936 PHE Chi-restraints excluded: chain D residue 1032 ASN 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 124 optimal weight: 5.9990 chunk 322 optimal weight: 30.0000 chunk 362 optimal weight: 8.9990 chunk 369 optimal weight: 4.9990 chunk 274 optimal weight: 0.9980 chunk 236 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1014 GLN A1017 ASN B1014 GLN B1017 ASN C1017 ASN D1017 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.066048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.048776 restraints weight = 112759.106| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 3.34 r_work: 0.2683 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1387 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= 0.191 Angle : 0.495 6.327 41500 Z= 0.256 Chirality : 0.036 0.126 4792 Planarity : 0.004 0.046 5228 Dihedral : 3.680 45.284 4242 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.93 % Allowed : 20.01 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.67 (0.14), residues: 3848 helix: 2.92 (0.10), residues: 2516 sheet: -0.48 (0.37), residues: 236 loop : -0.52 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 92 TYR 0.010 0.001 TYR D1015 PHE 0.016 0.001 PHE D 627 TRP 0.011 0.001 TRP C 680 HIS 0.004 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00433 (30488) covalent geometry : angle 0.49348 (41476) SS BOND : bond 0.00793 ( 12) SS BOND : angle 1.85003 ( 24) hydrogen bonds : bond 0.04363 ( 1890) hydrogen bonds : angle 3.94382 ( 5586) *********************** 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 219 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 134 time to evaluate : 1.349 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8182 (ttt-90) REVERT: A 509 MET cc_start: 0.8468 (mmp) cc_final: 0.8263 (mmp) REVERT: A 625 ASP cc_start: 0.9082 (m-30) cc_final: 0.8813 (m-30) REVERT: A 1017 ASN cc_start: 0.8090 (OUTLIER) cc_final: 0.7853 (t0) REVERT: A 1118 GLU cc_start: 0.9328 (OUTLIER) cc_final: 0.9086 (tm-30) REVERT: A 1156 ASP cc_start: 0.9204 (m-30) cc_final: 0.8870 (m-30) REVERT: B 92 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8701 (ttt-90) REVERT: B 643 LEU cc_start: 0.9674 (OUTLIER) cc_final: 0.9439 (mm) REVERT: B 872 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8822 (mm) REVERT: B 926 MET cc_start: 0.9123 (mmt) cc_final: 0.8887 (mmt) REVERT: B 1017 ASN cc_start: 0.8217 (OUTLIER) cc_final: 0.7753 (t0) REVERT: B 1037 ASN cc_start: 0.9381 (m-40) cc_final: 0.9141 (m-40) REVERT: B 1118 GLU cc_start: 0.9383 (OUTLIER) cc_final: 0.9110 (tm-30) REVERT: C 509 MET cc_start: 0.8565 (mmp) cc_final: 0.8359 (mmp) REVERT: C 872 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8897 (mm) REVERT: C 1118 GLU cc_start: 0.9369 (OUTLIER) cc_final: 0.9060 (pp20) REVERT: C 1156 ASP cc_start: 0.9202 (m-30) cc_final: 0.8860 (m-30) REVERT: D 92 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8689 (ttt-90) REVERT: D 284 MET cc_start: 0.9123 (mmm) cc_final: 0.8764 (mmm) REVERT: D 625 ASP cc_start: 0.9130 (m-30) cc_final: 0.8866 (m-30) outliers start: 85 outliers final: 45 residues processed: 201 average time/residue: 0.1829 time to fit residues: 62.4010 Evaluate side-chains 184 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 128 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 709 THR 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 1017 ASN Chi-restraints excluded: chain A residue 1118 GLU 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 787 VAL 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 909 ILE 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 B residue 1125 GLU Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 507 LEU 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 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 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 507 LEU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 709 THR 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 1032 ASN Chi-restraints excluded: chain D residue 1125 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 32 optimal weight: 8.9990 chunk 370 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 223 optimal weight: 20.0000 chunk 69 optimal weight: 9.9990 chunk 175 optimal weight: 0.8980 chunk 302 optimal weight: 7.9990 chunk 255 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 246 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1014 GLN A1017 ASN B1014 GLN B1017 ASN C1014 GLN C1161 GLN D1014 GLN ** D1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.065903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.048665 restraints weight = 113094.130| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.33 r_work: 0.2677 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1497 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= 0.188 Angle : 0.495 6.333 41500 Z= 0.255 Chirality : 0.036 0.126 4792 Planarity : 0.004 0.047 5228 Dihedral : 3.622 21.354 4240 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.93 % Allowed : 20.14 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.68 (0.14), residues: 3848 helix: 2.91 (0.10), residues: 2520 sheet: -0.46 (0.37), residues: 236 loop : -0.52 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 92 TYR 0.010 0.001 TYR D1015 PHE 0.015 0.001 PHE B 627 TRP 0.011 0.001 TRP C 680 HIS 0.004 0.001 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00428 (30488) covalent geometry : angle 0.49363 (41476) SS BOND : bond 0.00683 ( 12) SS BOND : angle 1.61941 ( 24) hydrogen bonds : bond 0.04235 ( 1890) hydrogen bonds : angle 3.90216 ( 5586) *********************** 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 215 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 130 time to evaluate : 1.315 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8163 (ttt-90) REVERT: A 625 ASP cc_start: 0.9114 (m-30) cc_final: 0.8842 (m-30) REVERT: A 784 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8383 (ttm) REVERT: A 1017 ASN cc_start: 0.8087 (OUTLIER) cc_final: 0.7855 (t0) REVERT: A 1118 GLU cc_start: 0.9338 (OUTLIER) cc_final: 0.9095 (tm-30) REVERT: B 92 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8650 (ttt-90) REVERT: B 643 LEU cc_start: 0.9677 (OUTLIER) cc_final: 0.9444 (mm) REVERT: B 872 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8800 (mm) REVERT: B 926 MET cc_start: 0.9145 (mmt) cc_final: 0.8896 (mmt) REVERT: B 1017 ASN cc_start: 0.8166 (OUTLIER) cc_final: 0.7746 (t0) REVERT: B 1037 ASN cc_start: 0.9361 (m-40) cc_final: 0.9098 (m-40) REVERT: B 1118 GLU cc_start: 0.9380 (OUTLIER) cc_final: 0.9108 (tm-30) REVERT: C 872 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8895 (mm) REVERT: C 1118 GLU cc_start: 0.9370 (OUTLIER) cc_final: 0.9058 (pp20) REVERT: C 1156 ASP cc_start: 0.9215 (m-30) cc_final: 0.8865 (m-30) REVERT: D 92 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8705 (ttt-90) REVERT: D 284 MET cc_start: 0.9100 (mmm) cc_final: 0.8798 (mmm) REVERT: D 625 ASP cc_start: 0.9152 (m-30) cc_final: 0.8879 (m-30) REVERT: D 784 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8419 (ttm) outliers start: 85 outliers final: 52 residues processed: 196 average time/residue: 0.1841 time to fit residues: 61.7090 Evaluate side-chains 192 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 127 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 370 SER 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 909 ILE Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1017 ASN Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1118 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 370 SER Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 643 LEU 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 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 B residue 1125 GLU Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 684 MET 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 872 LEU 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 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 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 370 SER 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 787 VAL 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 941 LEU Chi-restraints excluded: chain D residue 1032 ASN 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 312 optimal weight: 20.0000 chunk 270 optimal weight: 7.9990 chunk 333 optimal weight: 0.5980 chunk 198 optimal weight: 20.0000 chunk 187 optimal weight: 1.9990 chunk 279 optimal weight: 6.9990 chunk 288 optimal weight: 6.9990 chunk 276 optimal weight: 0.8980 chunk 330 optimal weight: 4.9990 chunk 251 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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** B1017 ASN C1017 ASN D1014 GLN ** D1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.065939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.048692 restraints weight = 111930.240| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 3.33 r_work: 0.2684 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1606 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= 0.174 Angle : 0.487 6.553 41500 Z= 0.251 Chirality : 0.036 0.124 4792 Planarity : 0.004 0.047 5228 Dihedral : 3.626 21.098 4240 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.89 % Allowed : 20.01 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.70 (0.14), residues: 3848 helix: 2.93 (0.10), residues: 2520 sheet: -0.47 (0.37), residues: 236 loop : -0.51 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 327 TYR 0.010 0.001 TYR B1015 PHE 0.015 0.001 PHE B 627 TRP 0.011 0.001 TRP B 680 HIS 0.003 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00396 (30488) covalent geometry : angle 0.48617 (41476) SS BOND : bond 0.00621 ( 12) SS BOND : angle 1.50620 ( 24) hydrogen bonds : bond 0.04107 ( 1890) hydrogen bonds : angle 3.85366 ( 5586) *********************** 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 213 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 129 time to evaluate : 1.315 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8228 (ttt-90) REVERT: A 625 ASP cc_start: 0.9127 (m-30) cc_final: 0.8851 (m-30) REVERT: A 784 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8269 (ttm) REVERT: B 92 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8215 (ttt-90) REVERT: B 643 LEU cc_start: 0.9678 (OUTLIER) cc_final: 0.9446 (mm) REVERT: B 872 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8780 (mm) REVERT: B 926 MET cc_start: 0.9143 (mmt) cc_final: 0.8924 (mmt) REVERT: B 1017 ASN cc_start: 0.7967 (OUTLIER) cc_final: 0.7675 (t0) REVERT: B 1037 ASN cc_start: 0.9341 (m-40) cc_final: 0.9075 (m-40) REVERT: B 1118 GLU cc_start: 0.9374 (OUTLIER) cc_final: 0.9097 (tm-30) REVERT: C 872 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8912 (mm) REVERT: C 1118 GLU cc_start: 0.9355 (OUTLIER) cc_final: 0.9055 (pp20) REVERT: C 1156 ASP cc_start: 0.9223 (m-30) cc_final: 0.8858 (m-30) REVERT: D 92 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8703 (ttt-90) REVERT: D 284 MET cc_start: 0.9089 (mmm) cc_final: 0.8885 (mmm) REVERT: D 509 MET cc_start: 0.8454 (mmp) cc_final: 0.8240 (mmp) REVERT: D 625 ASP cc_start: 0.9153 (m-30) cc_final: 0.8867 (m-30) REVERT: D 784 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8393 (ttm) outliers start: 84 outliers final: 57 residues processed: 194 average time/residue: 0.1783 time to fit residues: 59.9507 Evaluate side-chains 193 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 125 time to evaluate : 1.226 ------------------------------------------------------------------------------- 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 370 SER 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 787 VAL 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 1165 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 622 MET 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 867 CYS Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 909 ILE 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 B residue 1165 ILE Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 684 MET 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 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 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 370 SER 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 787 VAL 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 941 LEU Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1125 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 203 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 301 optimal weight: 6.9990 chunk 227 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 218 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 28 optimal weight: 30.0000 chunk 354 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1014 GLN ** 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 = 0.3343 r_free = 0.3343 target = 0.065165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.047699 restraints weight = 112523.869| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 3.43 r_work: 0.2650 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 30500 Z= 0.239 Angle : 0.530 6.451 41500 Z= 0.272 Chirality : 0.037 0.129 4792 Planarity : 0.004 0.048 5228 Dihedral : 3.666 21.921 4240 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.00 % Allowed : 20.35 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.65 (0.14), residues: 3848 helix: 2.89 (0.10), residues: 2520 sheet: -0.47 (0.37), residues: 236 loop : -0.54 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 92 TYR 0.011 0.001 TYR D1015 PHE 0.017 0.001 PHE D 627 TRP 0.012 0.001 TRP B 680 HIS 0.006 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00546 (30488) covalent geometry : angle 0.52940 (41476) SS BOND : bond 0.00573 ( 12) SS BOND : angle 1.42096 ( 24) hydrogen bonds : bond 0.04306 ( 1890) hydrogen bonds : angle 3.93172 ( 5586) *********************** 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 210 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 123 time to evaluate : 1.365 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8039 (ttt-90) REVERT: A 625 ASP cc_start: 0.9190 (m-30) cc_final: 0.8892 (m-30) REVERT: A 784 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8100 (ttm) REVERT: B 92 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.7881 (ttt180) REVERT: B 643 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9385 (mm) REVERT: B 872 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8578 (mm) REVERT: B 926 MET cc_start: 0.9004 (mmt) cc_final: 0.8710 (mmt) REVERT: B 1037 ASN cc_start: 0.9284 (m-40) cc_final: 0.9053 (m-40) REVERT: B 1118 GLU cc_start: 0.9455 (OUTLIER) cc_final: 0.9140 (tm-30) REVERT: C 509 MET cc_start: 0.8460 (mmp) cc_final: 0.8242 (mmp) REVERT: C 872 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8716 (mm) REVERT: C 1118 GLU cc_start: 0.9441 (OUTLIER) cc_final: 0.9109 (pp20) REVERT: D 92 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8181 (ttt-90) REVERT: D 284 MET cc_start: 0.9145 (mmm) cc_final: 0.8918 (mmm) REVERT: D 509 MET cc_start: 0.8485 (mmp) cc_final: 0.8215 (mmp) REVERT: D 625 ASP cc_start: 0.9240 (m-30) cc_final: 0.8982 (m-30) REVERT: D 784 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8096 (ttm) outliers start: 87 outliers final: 55 residues processed: 193 average time/residue: 0.1786 time to fit residues: 59.4496 Evaluate side-chains 186 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 121 time to evaluate : 1.324 ------------------------------------------------------------------------------- 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 370 SER 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 787 VAL 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 1165 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 622 MET 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 867 CYS Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 909 ILE 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 1088 LEU Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1118 GLU Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 684 MET 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 872 LEU 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 1017 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 1146 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 370 SER 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 909 ILE Chi-restraints excluded: chain D residue 1017 ASN Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1125 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 231 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 378 optimal weight: 0.8980 chunk 290 optimal weight: 0.9980 chunk 163 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 216 optimal weight: 4.9990 chunk 219 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 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** C1017 ASN D1014 GLN ** D1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.066924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.049562 restraints weight = 111295.665| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 3.44 r_work: 0.2699 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 30500 Z= 0.105 Angle : 0.451 6.555 41500 Z= 0.234 Chirality : 0.035 0.144 4792 Planarity : 0.003 0.046 5228 Dihedral : 3.594 19.153 4240 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.07 % Allowed : 20.94 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.78 (0.14), residues: 3848 helix: 2.97 (0.10), residues: 2528 sheet: -0.46 (0.37), residues: 236 loop : -0.44 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 92 TYR 0.007 0.001 TYR A1015 PHE 0.011 0.001 PHE B 627 TRP 0.012 0.001 TRP A1058 HIS 0.006 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00225 (30488) covalent geometry : angle 0.44979 (41476) SS BOND : bond 0.00550 ( 12) SS BOND : angle 1.44204 ( 24) hydrogen bonds : bond 0.03726 ( 1890) hydrogen bonds : angle 3.73179 ( 5586) *********************** 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 189 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 129 time to evaluate : 1.290 Fit side-chains REVERT: A 92 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8255 (ttt-90) REVERT: A 355 MET cc_start: 0.9549 (mmm) cc_final: 0.9247 (mmm) REVERT: A 625 ASP cc_start: 0.9167 (m-30) cc_final: 0.8798 (m-30) REVERT: A 784 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8031 (ttm) REVERT: B 92 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8171 (ttt-90) REVERT: B 643 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9337 (mm) REVERT: B 926 MET cc_start: 0.8926 (mmt) cc_final: 0.8694 (mmt) REVERT: B 1118 GLU cc_start: 0.9401 (OUTLIER) cc_final: 0.9086 (tm-30) REVERT: C 92 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8050 (ttt-90) REVERT: C 509 MET cc_start: 0.8465 (mmp) cc_final: 0.8233 (mmp) REVERT: C 1118 GLU cc_start: 0.9390 (OUTLIER) cc_final: 0.9065 (pp20) REVERT: C 1156 ASP cc_start: 0.9274 (m-30) cc_final: 0.8862 (m-30) REVERT: D 92 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8148 (ttt-90) REVERT: D 625 ASP cc_start: 0.9207 (m-30) cc_final: 0.8894 (m-30) REVERT: D 784 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8034 (ttm) outliers start: 60 outliers final: 37 residues processed: 178 average time/residue: 0.1840 time to fit residues: 55.9745 Evaluate side-chains 172 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 126 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG 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 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 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 370 SER 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 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 258 SER Chi-restraints excluded: chain C residue 709 THR 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 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 1146 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 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 1088 LEU 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 352 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 256 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 383 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 225 optimal weight: 30.0000 chunk 304 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.065507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.048084 restraints weight = 112137.083| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 3.43 r_work: 0.2659 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 30500 Z= 0.218 Angle : 0.523 9.714 41500 Z= 0.266 Chirality : 0.037 0.123 4792 Planarity : 0.004 0.048 5228 Dihedral : 3.603 20.691 4240 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.76 % Allowed : 21.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.77 (0.14), residues: 3848 helix: 2.99 (0.10), residues: 2512 sheet: -0.44 (0.37), residues: 236 loop : -0.47 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 92 TYR 0.012 0.001 TYR A1015 PHE 0.016 0.001 PHE D 627 TRP 0.011 0.001 TRP B 680 HIS 0.004 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00499 (30488) covalent geometry : angle 0.52204 (41476) SS BOND : bond 0.00529 ( 12) SS BOND : angle 1.35383 ( 24) hydrogen bonds : bond 0.04068 ( 1890) hydrogen bonds : angle 3.84721 ( 5586) *********************** 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 173 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 122 time to evaluate : 1.293 Fit side-chains REVERT: A 284 MET cc_start: 0.9142 (tpp) cc_final: 0.8577 (mtt) REVERT: A 355 MET cc_start: 0.9559 (mmm) cc_final: 0.9270 (mmm) REVERT: A 625 ASP cc_start: 0.9182 (m-30) cc_final: 0.8846 (m-30) REVERT: A 784 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8087 (ttm) REVERT: B 643 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9346 (mm) REVERT: B 926 MET cc_start: 0.8986 (mmt) cc_final: 0.8744 (mmt) REVERT: B 1118 GLU cc_start: 0.9440 (OUTLIER) cc_final: 0.9119 (tm-30) REVERT: C 509 MET cc_start: 0.8471 (mmp) cc_final: 0.8230 (mmp) REVERT: C 1118 GLU cc_start: 0.9435 (OUTLIER) cc_final: 0.9103 (pp20) REVERT: D 92 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8202 (ttt-90) REVERT: D 625 ASP cc_start: 0.9227 (m-30) cc_final: 0.8754 (m-30) REVERT: D 784 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8099 (ttm) outliers start: 51 outliers final: 35 residues processed: 162 average time/residue: 0.1711 time to fit residues: 49.1274 Evaluate side-chains 164 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 123 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 936 PHE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 370 SER 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 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 B residue 1165 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 709 THR 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 1088 LEU Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1118 GLU Chi-restraints excluded: chain C residue 1146 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 315 LEU 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 1032 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 6 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 349 optimal weight: 6.9990 chunk 266 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 374 optimal weight: 1.9990 chunk 326 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 D 505 HIS 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 = 0.3341 r_free = 0.3341 target = 0.065106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.047679 restraints weight = 112118.091| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 3.43 r_work: 0.2650 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 30500 Z= 0.228 Angle : 0.533 10.600 41500 Z= 0.271 Chirality : 0.037 0.132 4792 Planarity : 0.004 0.048 5228 Dihedral : 3.679 20.406 4240 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.96 % Allowed : 21.42 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.71 (0.14), residues: 3848 helix: 2.93 (0.10), residues: 2512 sheet: -0.40 (0.38), residues: 236 loop : -0.49 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 92 TYR 0.013 0.001 TYR B1015 PHE 0.016 0.001 PHE D 627 TRP 0.012 0.001 TRP C 680 HIS 0.016 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00519 (30488) covalent geometry : angle 0.53208 (41476) SS BOND : bond 0.00498 ( 12) SS BOND : angle 1.33985 ( 24) hydrogen bonds : bond 0.04193 ( 1890) hydrogen bonds : angle 3.89806 ( 5586) ********************** 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 176 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 119 time to evaluate : 1.306 Fit side-chains revert: symmetry clash REVERT: A 355 MET cc_start: 0.9570 (mmm) cc_final: 0.9281 (mmm) REVERT: A 625 ASP cc_start: 0.9184 (m-30) cc_final: 0.8873 (m-30) REVERT: A 784 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8094 (ttm) REVERT: B 92 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.7964 (ttt-90) REVERT: B 643 LEU cc_start: 0.9610 (OUTLIER) cc_final: 0.9371 (mm) REVERT: B 926 MET cc_start: 0.9015 (mmt) cc_final: 0.8732 (mmt) REVERT: B 1118 GLU cc_start: 0.9459 (OUTLIER) cc_final: 0.9148 (tm-30) REVERT: C 509 MET cc_start: 0.8494 (mmp) cc_final: 0.8246 (mmp) REVERT: C 1118 GLU cc_start: 0.9450 (OUTLIER) cc_final: 0.9116 (pp20) REVERT: D 625 ASP cc_start: 0.9234 (m-30) cc_final: 0.8929 (m-30) REVERT: D 784 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8088 (ttm) outliers start: 57 outliers final: 43 residues processed: 167 average time/residue: 0.1839 time to fit residues: 53.9578 Evaluate side-chains 167 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 118 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 370 SER 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 936 PHE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 370 SER 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 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 B residue 1125 GLU Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 370 SER 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 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 315 LEU Chi-restraints excluded: chain D residue 370 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 147 optimal weight: 4.9990 chunk 284 optimal weight: 3.9990 chunk 281 optimal weight: 0.7980 chunk 117 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 363 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 335 optimal weight: 8.9990 chunk 183 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D1017 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.066238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.048876 restraints weight = 111539.044| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 3.42 r_work: 0.2683 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 30500 Z= 0.109 Angle : 0.482 9.234 41500 Z= 0.246 Chirality : 0.035 0.272 4792 Planarity : 0.004 0.045 5228 Dihedral : 3.677 19.982 4240 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.65 % Allowed : 21.69 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.77 (0.14), residues: 3848 helix: 2.98 (0.10), residues: 2512 sheet: -0.42 (0.38), residues: 236 loop : -0.45 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 92 TYR 0.011 0.001 TYR B1015 PHE 0.012 0.001 PHE B 627 TRP 0.021 0.001 TRP C 579 HIS 0.003 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00232 (30488) covalent geometry : angle 0.48143 (41476) SS BOND : bond 0.00515 ( 12) SS BOND : angle 1.41414 ( 24) hydrogen bonds : bond 0.03896 ( 1890) hydrogen bonds : angle 3.77049 ( 5586) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7057.57 seconds wall clock time: 121 minutes 48.24 seconds (7308.24 seconds total)