Starting phenix.real_space_refine on Mon Aug 25 19:08:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b92_44366/08_2025/9b92_44366.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b92_44366/08_2025/9b92_44366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b92_44366/08_2025/9b92_44366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b92_44366/08_2025/9b92_44366.map" model { file = "/net/cci-nas-00/data/ceres_data/9b92_44366/08_2025/9b92_44366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b92_44366/08_2025/9b92_44366.cif" } resolution = 3.5 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 152 5.16 5 C 19404 2.51 5 N 5288 2.21 5 O 5100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.04s 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: 29948 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7486 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 43, 'TRANS': 946} Chain breaks: 9 Unresolved non-hydrogen bonds: 390 Unresolved non-hydrogen angles: 482 Unresolved non-hydrogen dihedrals: 316 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLU:plan': 19, 'GLN:plan1': 5, 'ARG:plan': 16, 'ASP:plan': 16, 'HIS:plan': 2, 'PHE:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 275 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 8.09, per 1000 atoms: 0.27 Number of scatterers: 29948 At special positions: 0 Unit cell: (164.772, 164.772, 161.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 152 16.00 O 5100 8.00 N 5288 7.00 C 19404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 37 " distance=2.97 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 37 " distance=2.97 Simple disulfide: pdb=" SG CYS C 35 " - pdb=" SG CYS C 37 " distance=2.97 Simple disulfide: pdb=" SG CYS D 35 " - pdb=" SG CYS D 37 " distance=2.97 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: 2.70 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7336 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 16 sheets defined 68.9% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 98 through 109 removed outlier: 4.007A pdb=" N VAL A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 150 removed outlier: 4.413A pdb=" N VAL A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 178 removed outlier: 3.571A pdb=" N HIS A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR A 178 " --> pdb=" O GLN A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 201 Processing helix chain 'A' and resid 246 through 260 Processing helix chain 'A' and resid 264 through 268 removed outlier: 3.585A pdb=" N GLY A 268 " --> pdb=" O GLY A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 Processing helix chain 'A' and resid 308 through 318 Processing helix chain 'A' and resid 325 through 337 removed outlier: 4.080A pdb=" N GLU A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 357 removed outlier: 4.517A pdb=" N GLN A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 386 removed outlier: 3.675A 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: 3.546A pdb=" N ALA A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 436 removed outlier: 3.838A pdb=" N SER A 428 " --> pdb=" O HIS A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 447 Processing helix chain 'A' and resid 456 through 466 Processing helix chain 'A' and resid 471 through 480 Processing helix chain 'A' and resid 502 through 512 removed outlier: 4.303A pdb=" N VAL A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 571 through 582 Processing helix chain 'A' and resid 584 through 602 Processing helix chain 'A' and resid 606 through 633 Processing helix chain 'A' and resid 635 through 645 removed outlier: 3.513A pdb=" N ALA A 639 " --> pdb=" O GLU A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 663 through 669 removed outlier: 3.853A pdb=" N GLN A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 681 Processing helix chain 'A' and resid 689 through 699 Processing helix chain 'A' and resid 700 through 705 Processing helix chain 'A' and resid 767 through 778 Processing helix chain 'A' and resid 778 through 803 Processing helix chain 'A' and resid 811 through 834 Processing helix chain 'A' and resid 852 through 862 removed outlier: 4.106A 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 905 removed outlier: 3.503A pdb=" N MET A 900 " --> pdb=" O CYS A 896 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG A 905 " --> pdb=" O VAL A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 912 removed outlier: 3.687A pdb=" N VAL A 912 " --> pdb=" O ILE A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 926 removed outlier: 3.726A pdb=" N LYS A 919 " --> pdb=" O GLN A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 953 Processing helix chain 'A' and resid 958 through 967 Processing helix chain 'A' and resid 967 through 974 removed outlier: 3.627A pdb=" N ILE A 974 " --> pdb=" O PRO A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 983 Processing helix chain 'A' and resid 984 through 988 Processing helix chain 'A' and resid 1016 through 1033 removed outlier: 3.833A pdb=" N VAL A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1050 Processing helix chain 'A' and resid 1050 through 1071 removed outlier: 4.293A pdb=" N TYR A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A1071 " --> pdb=" O ARG A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1088 removed outlier: 3.978A pdb=" N VAL A1081 " --> pdb=" O PRO A1077 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE A1082 " --> pdb=" O PRO A1078 " (cutoff:3.500A) removed outlier: 3.973A 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 removed outlier: 4.061A pdb=" N ARG A1177 " --> pdb=" O LYS A1173 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 98 through 109 removed outlier: 4.007A pdb=" N VAL B 102 " --> pdb=" O ASP B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 150 removed outlier: 4.413A pdb=" N VAL B 143 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 178 removed outlier: 3.571A pdb=" N HIS B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR B 178 " --> pdb=" O GLN B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 201 Processing helix chain 'B' and resid 246 through 260 Processing helix chain 'B' and resid 264 through 268 removed outlier: 3.585A pdb=" N GLY B 268 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 294 Processing helix chain 'B' and resid 308 through 318 Processing helix chain 'B' and resid 325 through 337 removed outlier: 4.080A pdb=" N GLU B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 357 removed outlier: 4.517A pdb=" N GLN B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 386 removed outlier: 3.674A 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: 3.545A pdb=" N ALA B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 436 removed outlier: 3.838A pdb=" N SER B 428 " --> pdb=" O HIS B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 447 Processing helix chain 'B' and resid 456 through 466 Processing helix chain 'B' and resid 471 through 480 Processing helix chain 'B' and resid 502 through 512 removed outlier: 4.303A pdb=" N VAL B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 570 Processing helix chain 'B' and resid 571 through 582 Processing helix chain 'B' and resid 584 through 602 Processing helix chain 'B' and resid 606 through 633 Processing helix chain 'B' and resid 635 through 645 removed outlier: 3.513A pdb=" N ALA B 639 " --> pdb=" O GLU B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 663 through 669 removed outlier: 3.853A pdb=" N GLN B 669 " --> pdb=" O ALA B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 681 Processing helix chain 'B' and resid 689 through 699 Processing helix chain 'B' and resid 700 through 705 Processing helix chain 'B' and resid 767 through 778 Processing helix chain 'B' and resid 778 through 803 Processing helix chain 'B' and resid 811 through 834 Processing helix chain 'B' and resid 852 through 862 removed outlier: 4.107A 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 905 removed outlier: 3.502A pdb=" N MET B 900 " --> pdb=" O CYS B 896 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG B 905 " --> pdb=" O VAL B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 912 removed outlier: 3.687A pdb=" N VAL B 912 " --> pdb=" O ILE B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 926 removed outlier: 3.726A pdb=" N LYS B 919 " --> pdb=" O GLN B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 953 Processing helix chain 'B' and resid 958 through 967 Processing helix chain 'B' and resid 967 through 974 removed outlier: 3.627A pdb=" N ILE B 974 " --> pdb=" O PRO B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 983 Processing helix chain 'B' and resid 984 through 988 Processing helix chain 'B' and resid 1016 through 1033 removed outlier: 3.833A pdb=" N VAL B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1050 Processing helix chain 'B' and resid 1050 through 1071 removed outlier: 4.293A pdb=" N TYR B1063 " --> pdb=" O LYS B1059 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG B1064 " --> pdb=" O ALA B1060 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER B1071 " --> pdb=" O ARG B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1088 removed outlier: 3.978A pdb=" N VAL B1081 " --> pdb=" O PRO B1077 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE B1082 " --> pdb=" O PRO B1078 " (cutoff:3.500A) removed outlier: 3.973A 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 removed outlier: 4.061A pdb=" N ARG B1177 " --> pdb=" O LYS B1173 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 15 Processing helix chain 'C' and resid 98 through 109 removed outlier: 4.007A pdb=" N VAL C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 150 removed outlier: 4.413A pdb=" N VAL C 143 " --> pdb=" O ARG C 139 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 178 removed outlier: 3.571A pdb=" N HIS C 165 " --> pdb=" O GLY C 161 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR C 178 " --> pdb=" O GLN C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 201 Processing helix chain 'C' and resid 246 through 260 Processing helix chain 'C' and resid 264 through 268 removed outlier: 3.585A pdb=" N GLY C 268 " --> pdb=" O GLY C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 294 Processing helix chain 'C' and resid 308 through 318 Processing helix chain 'C' and resid 325 through 337 removed outlier: 4.080A pdb=" N GLU C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 357 removed outlier: 4.517A pdb=" N GLN C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 386 removed outlier: 3.675A 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: 3.545A pdb=" N ALA C 409 " --> pdb=" O ARG C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 436 removed outlier: 3.837A pdb=" N SER C 428 " --> pdb=" O HIS C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 447 Processing helix chain 'C' and resid 456 through 466 Processing helix chain 'C' and resid 471 through 480 Processing helix chain 'C' and resid 502 through 512 removed outlier: 4.303A pdb=" N VAL C 506 " --> pdb=" O ASP C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 570 Processing helix chain 'C' and resid 571 through 582 Processing helix chain 'C' and resid 584 through 602 Processing helix chain 'C' and resid 606 through 633 Processing helix chain 'C' and resid 635 through 645 removed outlier: 3.513A pdb=" N ALA C 639 " --> pdb=" O GLU C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 663 through 669 removed outlier: 3.852A pdb=" N GLN C 669 " --> pdb=" O ALA C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 681 Processing helix chain 'C' and resid 689 through 699 Processing helix chain 'C' and resid 700 through 705 Processing helix chain 'C' and resid 767 through 778 Processing helix chain 'C' and resid 778 through 803 Processing helix chain 'C' and resid 811 through 834 Processing helix chain 'C' and resid 852 through 862 removed outlier: 4.107A 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 905 removed outlier: 3.503A pdb=" N MET C 900 " --> pdb=" O CYS C 896 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG C 905 " --> pdb=" O VAL C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 906 through 912 removed outlier: 3.687A pdb=" N VAL C 912 " --> pdb=" O ILE C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 926 removed outlier: 3.726A pdb=" N LYS C 919 " --> pdb=" O GLN C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 953 Processing helix chain 'C' and resid 958 through 967 Processing helix chain 'C' and resid 967 through 974 removed outlier: 3.627A pdb=" N ILE C 974 " --> pdb=" O PRO C 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 983 Processing helix chain 'C' and resid 984 through 988 Processing helix chain 'C' and resid 1016 through 1033 removed outlier: 3.833A pdb=" N VAL C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1050 Processing helix chain 'C' and resid 1050 through 1071 removed outlier: 4.293A pdb=" N TYR C1063 " --> pdb=" O LYS C1059 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG C1064 " --> pdb=" O ALA C1060 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER C1071 " --> pdb=" O ARG C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1088 removed outlier: 3.979A pdb=" N VAL C1081 " --> pdb=" O PRO C1077 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE C1082 " --> pdb=" O PRO C1078 " (cutoff:3.500A) removed outlier: 3.972A 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 removed outlier: 4.061A pdb=" N ARG C1177 " --> pdb=" O LYS C1173 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 98 through 109 removed outlier: 4.007A pdb=" N VAL D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 150 removed outlier: 4.412A pdb=" N VAL D 143 " --> pdb=" O ARG D 139 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG D 144 " --> pdb=" O ARG D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 178 removed outlier: 3.571A pdb=" N HIS D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR D 178 " --> pdb=" O GLN D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 201 Processing helix chain 'D' and resid 246 through 260 Processing helix chain 'D' and resid 264 through 268 removed outlier: 3.584A pdb=" N GLY D 268 " --> pdb=" O GLY D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 294 Processing helix chain 'D' and resid 308 through 318 Processing helix chain 'D' and resid 325 through 337 removed outlier: 4.080A pdb=" N GLU D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 357 removed outlier: 4.517A pdb=" N GLN D 348 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG D 357 " --> pdb=" O ARG D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 removed outlier: 3.675A 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: 3.546A pdb=" N ALA D 409 " --> pdb=" O ARG D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 436 removed outlier: 3.838A pdb=" N SER D 428 " --> pdb=" O HIS D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 447 Processing helix chain 'D' and resid 456 through 466 Processing helix chain 'D' and resid 471 through 480 Processing helix chain 'D' and resid 502 through 512 removed outlier: 4.303A pdb=" N VAL D 506 " --> pdb=" O ASP D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 570 Processing helix chain 'D' and resid 571 through 582 Processing helix chain 'D' and resid 584 through 602 Processing helix chain 'D' and resid 606 through 633 Processing helix chain 'D' and resid 635 through 645 removed outlier: 3.514A pdb=" N ALA D 639 " --> pdb=" O GLU D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 663 through 669 removed outlier: 3.853A pdb=" N GLN D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 681 Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 700 through 705 Processing helix chain 'D' and resid 767 through 778 Processing helix chain 'D' and resid 778 through 803 Processing helix chain 'D' and resid 811 through 834 Processing helix chain 'D' and resid 852 through 862 removed outlier: 4.107A 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 905 removed outlier: 3.503A pdb=" N MET D 900 " --> pdb=" O CYS D 896 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG D 905 " --> pdb=" O VAL D 901 " (cutoff:3.500A) Processing helix chain 'D' and resid 906 through 912 removed outlier: 3.687A pdb=" N VAL D 912 " --> pdb=" O ILE D 909 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 926 removed outlier: 3.726A pdb=" N LYS D 919 " --> pdb=" O GLN D 915 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 953 Processing helix chain 'D' and resid 958 through 967 Processing helix chain 'D' and resid 967 through 974 removed outlier: 3.627A pdb=" N ILE D 974 " --> pdb=" O PRO D 970 " (cutoff:3.500A) Processing helix chain 'D' and resid 979 through 983 Processing helix chain 'D' and resid 984 through 988 Processing helix chain 'D' and resid 1016 through 1033 removed outlier: 3.834A pdb=" N VAL D1020 " --> pdb=" O ALA D1016 " (cutoff:3.500A) Processing helix chain 'D' and resid 1033 through 1050 Processing helix chain 'D' and resid 1050 through 1071 removed outlier: 4.293A pdb=" N TYR D1063 " --> pdb=" O LYS D1059 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG D1064 " --> pdb=" O ALA D1060 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER D1071 " --> pdb=" O ARG D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1088 removed outlier: 3.979A pdb=" N VAL D1081 " --> pdb=" O PRO D1077 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE D1082 " --> pdb=" O PRO D1078 " (cutoff:3.500A) removed outlier: 3.972A 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 removed outlier: 4.061A pdb=" N ARG D1177 " --> pdb=" O LYS D1173 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 89 removed outlier: 8.158A pdb=" N TYR A 211 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ASP A 79 " --> pdb=" O TYR A 211 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 94 removed outlier: 6.321A pdb=" N LEU A 93 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA A 185 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N PHE A 233 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY A 187 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL A 235 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ALA A 189 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE A 153 " --> pdb=" O MET A 186 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL A 188 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR A 155 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL A 118 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU A 276 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N SER A 120 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LEU A 299 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU A 275 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL A 301 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU A 277 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N CYS A 298 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N TYR A 364 " --> pdb=" O CYS A 298 " (cutoff:3.500A) removed outlier: 7.189A 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: 4.245A 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 20 Processing sheet with id=AA6, first strand: chain 'B' and resid 88 through 89 removed outlier: 8.157A pdb=" N TYR B 211 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ASP B 79 " --> pdb=" O TYR B 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 92 through 94 removed outlier: 6.321A pdb=" N LEU B 93 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA B 185 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N PHE B 233 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY B 187 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL B 235 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA B 189 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE B 153 " --> pdb=" O MET B 186 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL B 188 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR B 155 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL B 118 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU B 276 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N SER B 120 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LEU B 299 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU B 275 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL B 301 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU B 277 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N CYS B 298 " --> pdb=" O THR B 362 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N TYR B 364 " --> pdb=" O CYS B 298 " (cutoff:3.500A) removed outlier: 7.189A 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: 4.245A 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 20 Processing sheet with id=AB1, first strand: chain 'C' and resid 88 through 89 removed outlier: 8.157A pdb=" N TYR C 211 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ASP C 79 " --> pdb=" O TYR C 211 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 92 through 94 removed outlier: 6.321A pdb=" N LEU C 93 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA C 185 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N PHE C 233 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY C 187 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL C 235 " --> pdb=" O GLY C 187 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ALA C 189 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE C 153 " --> pdb=" O MET C 186 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL C 188 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR C 155 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL C 118 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU C 276 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N SER C 120 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LEU C 299 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU C 275 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL C 301 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU C 277 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N CYS C 298 " --> pdb=" O THR C 362 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N TYR C 364 " --> pdb=" O CYS C 298 " (cutoff:3.500A) removed outlier: 7.189A 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: 4.245A 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 20 Processing sheet with id=AB5, first strand: chain 'D' and resid 88 through 89 removed outlier: 8.158A pdb=" N TYR D 211 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ASP D 79 " --> pdb=" O TYR D 211 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 92 through 94 removed outlier: 6.321A pdb=" N LEU D 93 " --> pdb=" O ASP D 236 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA D 185 " --> pdb=" O ALA D 231 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N PHE D 233 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY D 187 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL D 235 " --> pdb=" O GLY D 187 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ALA D 189 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE D 153 " --> pdb=" O MET D 186 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL D 188 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N THR D 155 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL D 118 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU D 276 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N SER D 120 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N LEU D 299 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU D 275 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL D 301 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU D 277 " --> pdb=" O VAL D 301 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N CYS D 298 " --> pdb=" O THR D 362 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N TYR D 364 " --> pdb=" O CYS D 298 " (cutoff:3.500A) removed outlier: 7.188A 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: 4.245A pdb=" N GLU D 989 " --> pdb=" O HIS D1002 " (cutoff:3.500A) 1916 hydrogen bonds defined for protein. 5568 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: 6.71 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9708 1.34 - 1.46: 7319 1.46 - 1.58: 13373 1.58 - 1.70: 0 1.70 - 1.82: 232 Bond restraints: 30632 Sorted by residual: bond pdb=" N ALA C 189 " pdb=" CA ALA C 189 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.18e-02 7.18e+03 8.25e+00 bond pdb=" N ALA A 189 " pdb=" CA ALA A 189 " ideal model delta sigma weight residual 1.453 1.486 -0.033 1.18e-02 7.18e+03 7.98e+00 bond pdb=" N ALA D 189 " pdb=" CA ALA D 189 " ideal model delta sigma weight residual 1.453 1.485 -0.033 1.18e-02 7.18e+03 7.67e+00 bond pdb=" N ALA B 189 " pdb=" CA ALA B 189 " ideal model delta sigma weight residual 1.453 1.485 -0.033 1.18e-02 7.18e+03 7.67e+00 bond pdb=" N ILE C 24 " pdb=" CA ILE C 24 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.29e-02 6.01e+03 7.32e+00 ... (remaining 30627 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 41226 2.52 - 5.04: 438 5.04 - 7.56: 12 7.56 - 10.08: 0 10.08 - 12.60: 4 Bond angle restraints: 41680 Sorted by residual: angle pdb=" N PRO A 604 " pdb=" CA PRO A 604 " pdb=" C PRO A 604 " ideal model delta sigma weight residual 114.80 102.20 12.60 1.42e+00 4.96e-01 7.88e+01 angle pdb=" N PRO D 604 " pdb=" CA PRO D 604 " pdb=" C PRO D 604 " ideal model delta sigma weight residual 114.80 102.20 12.60 1.42e+00 4.96e-01 7.88e+01 angle pdb=" N PRO B 604 " pdb=" CA PRO B 604 " pdb=" C PRO B 604 " ideal model delta sigma weight residual 114.80 102.22 12.58 1.42e+00 4.96e-01 7.85e+01 angle pdb=" N PRO C 604 " pdb=" CA PRO C 604 " pdb=" C PRO C 604 " ideal model delta sigma weight residual 114.80 102.23 12.57 1.42e+00 4.96e-01 7.83e+01 angle pdb=" CA ASP B 605 " pdb=" C ASP B 605 " pdb=" O ASP B 605 " ideal model delta sigma weight residual 120.55 115.57 4.98 1.06e+00 8.90e-01 2.21e+01 ... (remaining 41675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 16700 15.87 - 31.73: 980 31.73 - 47.60: 192 47.60 - 63.46: 76 63.46 - 79.33: 16 Dihedral angle restraints: 17964 sinusoidal: 6620 harmonic: 11344 Sorted by residual: dihedral pdb=" CB CYS C 35 " pdb=" SG CYS C 35 " pdb=" SG CYS C 37 " pdb=" CB CYS C 37 " ideal model delta sinusoidal sigma weight residual 93.00 141.27 -48.27 1 1.00e+01 1.00e-02 3.21e+01 dihedral pdb=" CB CYS D 35 " pdb=" SG CYS D 35 " pdb=" SG CYS D 37 " pdb=" CB CYS D 37 " ideal model delta sinusoidal sigma weight residual 93.00 141.26 -48.26 1 1.00e+01 1.00e-02 3.21e+01 dihedral pdb=" CB CYS A 35 " pdb=" SG CYS A 35 " pdb=" SG CYS A 37 " pdb=" CB CYS A 37 " ideal model delta sinusoidal sigma weight residual 93.00 141.26 -48.26 1 1.00e+01 1.00e-02 3.21e+01 ... (remaining 17961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 3891 0.042 - 0.085: 705 0.085 - 0.127: 196 0.127 - 0.170: 9 0.170 - 0.212: 7 Chirality restraints: 4808 Sorted by residual: chirality pdb=" CA ILE B 24 " pdb=" N ILE B 24 " pdb=" C ILE B 24 " pdb=" CB ILE B 24 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ILE C 24 " pdb=" N ILE C 24 " pdb=" C ILE C 24 " pdb=" CB ILE C 24 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.10e+00 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 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 4805 not shown) Planarity restraints: 5264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 138 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" C LEU C 138 " -0.029 2.00e-02 2.50e+03 pdb=" O LEU C 138 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG C 139 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 138 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C LEU B 138 " -0.029 2.00e-02 2.50e+03 pdb=" O LEU B 138 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG B 139 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 138 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C LEU A 138 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU A 138 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG A 139 " -0.010 2.00e-02 2.50e+03 ... (remaining 5261 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 541 2.67 - 3.23: 31946 3.23 - 3.79: 48705 3.79 - 4.34: 60430 4.34 - 4.90: 100611 Nonbonded interactions: 242233 Sorted by model distance: nonbonded pdb=" OE2 GLU A 828 " pdb="CA CA A2001 " model vdw 2.118 2.510 nonbonded pdb=" OE2 GLU D 828 " pdb="CA CA D2001 " model vdw 2.118 2.510 nonbonded pdb=" OE2 GLU B 828 " pdb="CA CA B2001 " model vdw 2.118 2.510 nonbonded pdb=" OE2 GLU C 828 " pdb="CA CA C2001 " model vdw 2.118 2.510 nonbonded pdb=" OD1 ASN C 865 " pdb="CA CA C2001 " model vdw 2.128 2.510 ... (remaining 242228 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.960 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: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 28.200 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 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 : 0.012 0.941 30636 Z= 0.623 Angle : 0.728 28.508 41688 Z= 0.425 Chirality : 0.037 0.212 4808 Planarity : 0.004 0.036 5264 Dihedral : 11.398 79.326 10616 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.65 % Allowed : 5.52 % Favored : 93.83 % 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: 2.12 (0.14), residues: 3880 helix: 2.42 (0.10), residues: 2456 sheet: -0.13 (0.35), residues: 256 loop : -0.44 (0.19), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 140 TYR 0.010 0.001 TYR A 577 PHE 0.009 0.001 PHE D 899 TRP 0.011 0.001 TRP A 191 HIS 0.005 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00589 (30632) covalent geometry : angle 0.62687 (41680) SS BOND : bond 0.94093 ( 4) SS BOND : angle 26.71579 ( 8) hydrogen bonds : bond 0.11579 ( 1916) hydrogen bonds : angle 5.56009 ( 5568) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 1.193 Fit side-chains REVERT: A 625 ASP cc_start: 0.8983 (m-30) cc_final: 0.8720 (m-30) REVERT: A 877 LEU cc_start: 0.9601 (tt) cc_final: 0.9025 (tp) REVERT: B 284 MET cc_start: 0.7379 (mtp) cc_final: 0.6923 (mmt) REVERT: B 625 ASP cc_start: 0.8976 (m-30) cc_final: 0.8662 (m-30) REVERT: B 877 LEU cc_start: 0.9577 (tt) cc_final: 0.8976 (tp) REVERT: C 625 ASP cc_start: 0.8984 (m-30) cc_final: 0.8672 (m-30) REVERT: C 877 LEU cc_start: 0.9579 (tt) cc_final: 0.8978 (tp) REVERT: D 625 ASP cc_start: 0.8980 (m-30) cc_final: 0.8723 (m-30) REVERT: D 877 LEU cc_start: 0.9600 (tt) cc_final: 0.9029 (tp) outliers start: 19 outliers final: 4 residues processed: 203 average time/residue: 0.1781 time to fit residues: 59.9803 Evaluate side-chains 153 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 149 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain D residue 24 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.0170 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.6980 overall best weight: 3.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS A 669 GLN A 973 GLN A1051 GLN A1061 GLN B 240 HIS B 669 GLN B 973 GLN B1051 GLN B1061 GLN C 240 HIS C 669 GLN C 973 GLN C1051 GLN C1061 GLN D 240 HIS D 669 GLN D 973 GLN D1051 GLN D1061 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.066652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.048603 restraints weight = 148212.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.050153 restraints weight = 67407.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.051216 restraints weight = 41275.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.051953 restraints weight = 30239.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.052216 restraints weight = 24366.038| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30636 Z= 0.180 Angle : 0.542 5.939 41688 Z= 0.275 Chirality : 0.037 0.129 4808 Planarity : 0.004 0.034 5264 Dihedral : 4.115 58.863 4272 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.93 % Allowed : 8.47 % Favored : 90.60 % 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: 2.43 (0.14), residues: 3880 helix: 2.63 (0.10), residues: 2496 sheet: 0.66 (0.36), residues: 244 loop : -0.55 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 892 TYR 0.008 0.001 TYR A 211 PHE 0.013 0.001 PHE D 627 TRP 0.012 0.001 TRP C 191 HIS 0.004 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00406 (30632) covalent geometry : angle 0.54178 (41680) SS BOND : bond 0.02049 ( 4) SS BOND : angle 0.70696 ( 8) hydrogen bonds : bond 0.03821 ( 1916) hydrogen bonds : angle 4.44976 ( 5568) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 1.232 Fit side-chains REVERT: A 599 MET cc_start: 0.8520 (ttp) cc_final: 0.8228 (ttm) REVERT: A 622 MET cc_start: 0.8369 (ttm) cc_final: 0.7858 (ttm) REVERT: A 625 ASP cc_start: 0.9031 (m-30) cc_final: 0.8713 (m-30) REVERT: B 284 MET cc_start: 0.7424 (OUTLIER) cc_final: 0.6978 (mmt) REVERT: B 599 MET cc_start: 0.8524 (ttp) cc_final: 0.8205 (ttm) REVERT: B 622 MET cc_start: 0.8380 (ttm) cc_final: 0.7855 (ttm) REVERT: B 625 ASP cc_start: 0.9033 (m-30) cc_final: 0.8720 (m-30) REVERT: C 284 MET cc_start: 0.7087 (mtp) cc_final: 0.6844 (mmt) REVERT: C 599 MET cc_start: 0.8509 (ttp) cc_final: 0.8209 (ttm) REVERT: C 622 MET cc_start: 0.8405 (ttm) cc_final: 0.7922 (ttm) REVERT: C 625 ASP cc_start: 0.9029 (m-30) cc_final: 0.8729 (m-30) REVERT: D 599 MET cc_start: 0.8508 (ttp) cc_final: 0.8202 (ttm) REVERT: D 622 MET cc_start: 0.8389 (ttm) cc_final: 0.7891 (ttm) REVERT: D 625 ASP cc_start: 0.9028 (m-30) cc_final: 0.8718 (m-30) outliers start: 27 outliers final: 12 residues processed: 174 average time/residue: 0.1641 time to fit residues: 50.1551 Evaluate side-chains 157 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 614 ASP Chi-restraints excluded: chain D residue 1034 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 290 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 389 optimal weight: 9.9990 chunk 351 optimal weight: 6.9990 chunk 265 optimal weight: 7.9990 chunk 215 optimal weight: 9.9990 chunk 136 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 179 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 202 optimal weight: 5.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 479 GLN D 479 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.065615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.047434 restraints weight = 149622.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.048947 restraints weight = 69139.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.050000 restraints weight = 42854.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.050685 restraints weight = 31363.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.051170 restraints weight = 25607.284| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 30636 Z= 0.257 Angle : 0.594 7.090 41688 Z= 0.293 Chirality : 0.037 0.128 4808 Planarity : 0.004 0.043 5264 Dihedral : 4.037 48.828 4272 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.23 % Allowed : 10.60 % Favored : 88.17 % 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: 2.28 (0.14), residues: 3880 helix: 2.54 (0.10), residues: 2492 sheet: 0.32 (0.37), residues: 232 loop : -0.57 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 892 TYR 0.009 0.001 TYR C 577 PHE 0.015 0.001 PHE C 627 TRP 0.010 0.001 TRP C1124 HIS 0.003 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00571 (30632) covalent geometry : angle 0.59411 (41680) SS BOND : bond 0.00694 ( 4) SS BOND : angle 0.62186 ( 8) hydrogen bonds : bond 0.03790 ( 1916) hydrogen bonds : angle 4.42552 ( 5568) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 1.213 Fit side-chains REVERT: A 581 MET cc_start: 0.9042 (mmp) cc_final: 0.8840 (mmp) REVERT: A 599 MET cc_start: 0.8586 (ttp) cc_final: 0.8334 (ttm) REVERT: A 622 MET cc_start: 0.8438 (ttm) cc_final: 0.8020 (ttm) REVERT: A 625 ASP cc_start: 0.9057 (m-30) cc_final: 0.8778 (m-30) REVERT: B 284 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.6911 (mmt) REVERT: B 599 MET cc_start: 0.8616 (ttp) cc_final: 0.8331 (ttm) REVERT: B 622 MET cc_start: 0.8444 (ttm) cc_final: 0.7989 (ttm) REVERT: B 625 ASP cc_start: 0.9048 (m-30) cc_final: 0.8771 (m-30) REVERT: C 284 MET cc_start: 0.7329 (mtp) cc_final: 0.6917 (mmt) REVERT: C 599 MET cc_start: 0.8598 (ttp) cc_final: 0.8314 (ttm) REVERT: C 622 MET cc_start: 0.8495 (ttm) cc_final: 0.8023 (ttm) REVERT: C 625 ASP cc_start: 0.9053 (m-30) cc_final: 0.8750 (m-30) REVERT: D 599 MET cc_start: 0.8614 (ttp) cc_final: 0.8326 (ttm) REVERT: D 622 MET cc_start: 0.8456 (ttm) cc_final: 0.8016 (ttm) REVERT: D 625 ASP cc_start: 0.9057 (m-30) cc_final: 0.8776 (m-30) outliers start: 36 outliers final: 17 residues processed: 170 average time/residue: 0.1535 time to fit residues: 44.7580 Evaluate side-chains 162 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 614 ASP Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 1034 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 393 optimal weight: 3.9990 chunk 394 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 chunk 137 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 231 optimal weight: 30.0000 chunk 37 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 242 optimal weight: 9.9990 chunk 310 optimal weight: 0.2980 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 669 GLN B 669 GLN C 669 GLN D 669 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.067040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.049214 restraints weight = 147838.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.050770 restraints weight = 66845.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.051847 restraints weight = 40522.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.052585 restraints weight = 29531.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.053011 restraints weight = 23968.966| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30636 Z= 0.118 Angle : 0.473 6.387 41688 Z= 0.239 Chirality : 0.035 0.127 4808 Planarity : 0.004 0.043 5264 Dihedral : 3.643 22.378 4264 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.13 % Allowed : 11.08 % Favored : 87.79 % 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: 2.47 (0.14), residues: 3880 helix: 2.70 (0.11), residues: 2496 sheet: 0.39 (0.36), residues: 232 loop : -0.54 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 327 TYR 0.006 0.001 TYR A 211 PHE 0.015 0.001 PHE C 627 TRP 0.009 0.001 TRP A 772 HIS 0.002 0.000 HIS C 424 Details of bonding type rmsd covalent geometry : bond 0.00263 (30632) covalent geometry : angle 0.47313 (41680) SS BOND : bond 0.00083 ( 4) SS BOND : angle 0.67412 ( 8) hydrogen bonds : bond 0.03330 ( 1916) hydrogen bonds : angle 4.10173 ( 5568) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 MET cc_start: 0.8593 (ttp) cc_final: 0.8361 (ttm) REVERT: A 622 MET cc_start: 0.8417 (ttm) cc_final: 0.8032 (ttm) REVERT: A 625 ASP cc_start: 0.9051 (m-30) cc_final: 0.8778 (m-30) REVERT: B 284 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.6938 (mmt) REVERT: B 599 MET cc_start: 0.8614 (ttp) cc_final: 0.8311 (ttm) REVERT: B 622 MET cc_start: 0.8413 (ttm) cc_final: 0.8029 (ttm) REVERT: B 625 ASP cc_start: 0.9045 (m-30) cc_final: 0.8757 (m-30) REVERT: C 284 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.7004 (mmt) REVERT: C 599 MET cc_start: 0.8592 (ttp) cc_final: 0.8357 (ttm) REVERT: C 622 MET cc_start: 0.8412 (ttm) cc_final: 0.8096 (ttm) REVERT: C 625 ASP cc_start: 0.9038 (m-30) cc_final: 0.8754 (m-30) REVERT: D 599 MET cc_start: 0.8596 (ttp) cc_final: 0.8379 (ttm) REVERT: D 622 MET cc_start: 0.8417 (ttm) cc_final: 0.8025 (ttm) REVERT: D 625 ASP cc_start: 0.9041 (m-30) cc_final: 0.8751 (m-30) outliers start: 33 outliers final: 14 residues processed: 183 average time/residue: 0.1727 time to fit residues: 53.4599 Evaluate side-chains 165 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain D residue 614 ASP Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 983 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 211 optimal weight: 0.7980 chunk 303 optimal weight: 30.0000 chunk 41 optimal weight: 10.0000 chunk 218 optimal weight: 9.9990 chunk 263 optimal weight: 0.6980 chunk 356 optimal weight: 9.9990 chunk 209 optimal weight: 6.9990 chunk 281 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 200 optimal weight: 10.0000 chunk 244 optimal weight: 0.3980 overall best weight: 3.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A1084 HIS B 116 ASN B1084 HIS C 116 ASN ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.066011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.047946 restraints weight = 149384.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.049459 restraints weight = 68878.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.050511 restraints weight = 42773.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.051224 restraints weight = 31350.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.051613 restraints weight = 25486.016| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 30636 Z= 0.184 Angle : 0.533 8.259 41688 Z= 0.261 Chirality : 0.036 0.146 4808 Planarity : 0.004 0.045 5264 Dihedral : 3.632 23.157 4264 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.23 % Allowed : 12.11 % Favored : 86.66 % 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: 2.46 (0.14), residues: 3880 helix: 2.67 (0.11), residues: 2508 sheet: -0.35 (0.36), residues: 232 loop : -0.35 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1138 TYR 0.007 0.001 TYR A1063 PHE 0.015 0.001 PHE B 910 TRP 0.009 0.001 TRP C1124 HIS 0.004 0.001 HIS D1084 Details of bonding type rmsd covalent geometry : bond 0.00414 (30632) covalent geometry : angle 0.53286 (41680) SS BOND : bond 0.00236 ( 4) SS BOND : angle 0.69623 ( 8) hydrogen bonds : bond 0.03384 ( 1916) hydrogen bonds : angle 4.13283 ( 5568) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 MET cc_start: 0.9240 (tpp) cc_final: 0.8917 (tpp) REVERT: A 581 MET cc_start: 0.8977 (mmp) cc_final: 0.8659 (mmp) REVERT: A 622 MET cc_start: 0.8459 (ttm) cc_final: 0.8024 (ttm) REVERT: A 625 ASP cc_start: 0.9021 (m-30) cc_final: 0.8736 (m-30) REVERT: A 927 MET cc_start: 0.8376 (mmt) cc_final: 0.8081 (mmp) REVERT: B 284 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.7019 (mmt) REVERT: B 599 MET cc_start: 0.8683 (ttp) cc_final: 0.8482 (ttm) REVERT: B 622 MET cc_start: 0.8472 (ttm) cc_final: 0.8064 (ttm) REVERT: B 625 ASP cc_start: 0.9000 (m-30) cc_final: 0.8708 (m-30) REVERT: B 927 MET cc_start: 0.8379 (mmt) cc_final: 0.8081 (mmp) REVERT: C 284 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.6993 (mmt) REVERT: C 576 MET cc_start: 0.9203 (tpp) cc_final: 0.8941 (tpp) REVERT: C 622 MET cc_start: 0.8452 (ttm) cc_final: 0.8067 (ttm) REVERT: C 625 ASP cc_start: 0.9021 (m-30) cc_final: 0.8743 (m-30) REVERT: D 576 MET cc_start: 0.9235 (tpp) cc_final: 0.8909 (tpp) REVERT: D 599 MET cc_start: 0.8691 (ttp) cc_final: 0.8486 (ttm) REVERT: D 622 MET cc_start: 0.8460 (ttm) cc_final: 0.8019 (ttm) REVERT: D 625 ASP cc_start: 0.9020 (m-30) cc_final: 0.8740 (m-30) outliers start: 36 outliers final: 24 residues processed: 168 average time/residue: 0.1699 time to fit residues: 48.8718 Evaluate side-chains 164 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 983 MET Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain D residue 20 CYS Chi-restraints excluded: chain D residue 614 ASP Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 1035 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 85 optimal weight: 1.9990 chunk 315 optimal weight: 8.9990 chunk 305 optimal weight: 10.0000 chunk 379 optimal weight: 0.6980 chunk 38 optimal weight: 20.0000 chunk 358 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 391 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 246 optimal weight: 0.9980 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1084 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.066344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.048627 restraints weight = 149516.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.050133 restraints weight = 70133.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.051093 restraints weight = 43745.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.051865 restraints weight = 32497.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.052337 restraints weight = 26374.707| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30636 Z= 0.170 Angle : 0.515 6.528 41688 Z= 0.254 Chirality : 0.035 0.118 4808 Planarity : 0.004 0.048 5264 Dihedral : 3.639 22.770 4264 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.17 % Allowed : 12.76 % Favored : 86.08 % 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: 2.49 (0.14), residues: 3880 helix: 2.71 (0.10), residues: 2504 sheet: -0.49 (0.35), residues: 236 loop : -0.32 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 612 TYR 0.007 0.001 TYR A1063 PHE 0.014 0.001 PHE C 627 TRP 0.009 0.001 TRP C1124 HIS 0.004 0.001 HIS C1002 Details of bonding type rmsd covalent geometry : bond 0.00384 (30632) covalent geometry : angle 0.51529 (41680) SS BOND : bond 0.00262 ( 4) SS BOND : angle 0.68106 ( 8) hydrogen bonds : bond 0.03318 ( 1916) hydrogen bonds : angle 4.07770 ( 5568) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 MET cc_start: 0.9227 (tpp) cc_final: 0.8896 (tpp) REVERT: A 581 MET cc_start: 0.9037 (mmp) cc_final: 0.8706 (mmp) REVERT: A 599 MET cc_start: 0.8718 (ttm) cc_final: 0.8516 (ttm) REVERT: A 622 MET cc_start: 0.8504 (ttm) cc_final: 0.8044 (ttm) REVERT: A 625 ASP cc_start: 0.9035 (m-30) cc_final: 0.8730 (m-30) REVERT: A 927 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8058 (mmp) REVERT: A 988 MET cc_start: 0.7732 (mtp) cc_final: 0.7437 (mtp) REVERT: B 284 MET cc_start: 0.7434 (OUTLIER) cc_final: 0.7028 (mmt) REVERT: B 576 MET cc_start: 0.9252 (tpp) cc_final: 0.8915 (tpp) REVERT: B 599 MET cc_start: 0.8741 (ttp) cc_final: 0.8515 (ttm) REVERT: B 622 MET cc_start: 0.8508 (ttm) cc_final: 0.8050 (ttm) REVERT: B 625 ASP cc_start: 0.9032 (m-30) cc_final: 0.8730 (m-30) REVERT: B 927 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8052 (mmp) REVERT: C 284 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.7001 (mmt) REVERT: C 576 MET cc_start: 0.9235 (tpp) cc_final: 0.8947 (tpp) REVERT: C 599 MET cc_start: 0.8744 (ttm) cc_final: 0.8523 (ttm) REVERT: C 622 MET cc_start: 0.8501 (ttm) cc_final: 0.8075 (ttm) REVERT: C 625 ASP cc_start: 0.9034 (m-30) cc_final: 0.8720 (m-30) REVERT: D 576 MET cc_start: 0.9259 (tpp) cc_final: 0.8919 (tpp) REVERT: D 599 MET cc_start: 0.8733 (ttp) cc_final: 0.8488 (ttm) REVERT: D 622 MET cc_start: 0.8508 (ttm) cc_final: 0.8042 (ttm) REVERT: D 625 ASP cc_start: 0.9053 (m-30) cc_final: 0.8764 (m-30) outliers start: 34 outliers final: 30 residues processed: 170 average time/residue: 0.1674 time to fit residues: 49.2360 Evaluate side-chains 173 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 927 MET Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1035 LEU Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 983 MET Chi-restraints excluded: chain B residue 1035 LEU Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain D residue 20 CYS Chi-restraints excluded: chain D residue 614 ASP Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 983 MET Chi-restraints excluded: chain D residue 1035 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 335 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 196 optimal weight: 2.9990 chunk 345 optimal weight: 0.7980 chunk 16 optimal weight: 20.0000 chunk 120 optimal weight: 30.0000 chunk 66 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 84 optimal weight: 0.6980 chunk 205 optimal weight: 0.6980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.067129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.049233 restraints weight = 147727.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.050791 restraints weight = 67759.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.051891 restraints weight = 41660.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.052599 restraints weight = 30294.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.053065 restraints weight = 24601.675| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 30636 Z= 0.099 Angle : 0.462 6.781 41688 Z= 0.232 Chirality : 0.034 0.120 4808 Planarity : 0.004 0.052 5264 Dihedral : 3.542 20.581 4264 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.06 % Allowed : 13.20 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.58 (0.14), residues: 3880 helix: 2.78 (0.11), residues: 2508 sheet: -0.59 (0.35), residues: 240 loop : -0.28 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1138 TYR 0.005 0.001 TYR B 211 PHE 0.016 0.001 PHE B 910 TRP 0.010 0.001 TRP C 772 HIS 0.004 0.001 HIS D1002 Details of bonding type rmsd covalent geometry : bond 0.00219 (30632) covalent geometry : angle 0.46165 (41680) SS BOND : bond 0.00336 ( 4) SS BOND : angle 0.68523 ( 8) hydrogen bonds : bond 0.03047 ( 1916) hydrogen bonds : angle 3.91142 ( 5568) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 MET cc_start: 0.9254 (tpp) cc_final: 0.8957 (tpp) REVERT: A 599 MET cc_start: 0.8740 (ttm) cc_final: 0.8499 (ttm) REVERT: A 622 MET cc_start: 0.8444 (ttm) cc_final: 0.8086 (ttm) REVERT: A 625 ASP cc_start: 0.8973 (m-30) cc_final: 0.8692 (m-30) REVERT: B 284 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6944 (mmt) REVERT: B 576 MET cc_start: 0.9278 (tpp) cc_final: 0.8971 (tpp) REVERT: B 622 MET cc_start: 0.8453 (ttm) cc_final: 0.8098 (ttm) REVERT: B 625 ASP cc_start: 0.8976 (m-30) cc_final: 0.8696 (m-30) REVERT: C 284 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.7043 (mmt) REVERT: C 576 MET cc_start: 0.9255 (tpp) cc_final: 0.9002 (tpp) REVERT: C 599 MET cc_start: 0.8733 (ttm) cc_final: 0.8493 (ttm) REVERT: C 622 MET cc_start: 0.8453 (ttm) cc_final: 0.8124 (ttm) REVERT: C 625 ASP cc_start: 0.8983 (m-30) cc_final: 0.8686 (m-30) REVERT: D 576 MET cc_start: 0.9271 (tpp) cc_final: 0.8962 (tpp) REVERT: D 599 MET cc_start: 0.8755 (ttp) cc_final: 0.8553 (ttm) REVERT: D 622 MET cc_start: 0.8443 (ttm) cc_final: 0.8082 (ttm) REVERT: D 625 ASP cc_start: 0.8991 (m-30) cc_final: 0.8697 (m-30) outliers start: 31 outliers final: 21 residues processed: 177 average time/residue: 0.1767 time to fit residues: 53.4508 Evaluate side-chains 170 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain D residue 20 CYS Chi-restraints excluded: chain D residue 614 ASP Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 983 MET Chi-restraints excluded: chain D residue 1034 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 322 optimal weight: 0.7980 chunk 253 optimal weight: 0.0060 chunk 376 optimal weight: 2.9990 chunk 288 optimal weight: 9.9990 chunk 244 optimal weight: 0.0980 chunk 133 optimal weight: 10.0000 chunk 128 optimal weight: 40.0000 chunk 69 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 189 optimal weight: 8.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.067028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.049935 restraints weight = 148175.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.051472 restraints weight = 68714.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.052513 restraints weight = 42431.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.053223 restraints weight = 31239.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.053609 restraints weight = 25468.693| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 30636 Z= 0.100 Angle : 0.479 7.866 41688 Z= 0.237 Chirality : 0.034 0.122 4808 Planarity : 0.004 0.056 5264 Dihedral : 3.491 20.070 4264 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.75 % Allowed : 13.27 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.56 (0.14), residues: 3880 helix: 2.80 (0.10), residues: 2508 sheet: -0.90 (0.31), residues: 292 loop : -0.22 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1138 TYR 0.005 0.001 TYR B1063 PHE 0.012 0.001 PHE C 627 TRP 0.009 0.001 TRP C 772 HIS 0.007 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00222 (30632) covalent geometry : angle 0.47874 (41680) SS BOND : bond 0.00353 ( 4) SS BOND : angle 0.68996 ( 8) hydrogen bonds : bond 0.02976 ( 1916) hydrogen bonds : angle 3.91482 ( 5568) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 MET cc_start: 0.9271 (tpp) cc_final: 0.8967 (tpp) REVERT: A 599 MET cc_start: 0.8680 (ttm) cc_final: 0.8440 (ttm) REVERT: A 622 MET cc_start: 0.8507 (ttm) cc_final: 0.8125 (ttm) REVERT: A 625 ASP cc_start: 0.9036 (m-30) cc_final: 0.8739 (m-30) REVERT: B 284 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6952 (mmt) REVERT: B 576 MET cc_start: 0.9279 (tpp) cc_final: 0.8977 (tpp) REVERT: B 599 MET cc_start: 0.8765 (ttm) cc_final: 0.8550 (ttm) REVERT: B 622 MET cc_start: 0.8505 (ttm) cc_final: 0.8121 (ttm) REVERT: B 625 ASP cc_start: 0.9038 (m-30) cc_final: 0.8745 (m-30) REVERT: C 284 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.6982 (mmt) REVERT: C 576 MET cc_start: 0.9271 (tpp) cc_final: 0.9010 (tpp) REVERT: C 599 MET cc_start: 0.8714 (ttm) cc_final: 0.8464 (ttm) REVERT: C 622 MET cc_start: 0.8510 (ttm) cc_final: 0.8161 (ttm) REVERT: C 625 ASP cc_start: 0.9047 (m-30) cc_final: 0.8747 (m-30) REVERT: D 576 MET cc_start: 0.9269 (tpp) cc_final: 0.8967 (tpp) REVERT: D 599 MET cc_start: 0.8754 (ttp) cc_final: 0.8495 (ttm) REVERT: D 622 MET cc_start: 0.8488 (ttm) cc_final: 0.8096 (ttm) REVERT: D 625 ASP cc_start: 0.9041 (m-30) cc_final: 0.8741 (m-30) outliers start: 22 outliers final: 18 residues processed: 165 average time/residue: 0.1751 time to fit residues: 50.0999 Evaluate side-chains 166 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain D residue 20 CYS Chi-restraints excluded: chain D residue 614 ASP Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 983 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 170 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 299 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 360 optimal weight: 1.9990 chunk 331 optimal weight: 0.0970 chunk 314 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1037 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 = 0.3493 r_free = 0.3493 target = 0.066651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.049080 restraints weight = 149691.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.050602 restraints weight = 69326.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.051662 restraints weight = 42996.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.052406 restraints weight = 31615.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.052776 restraints weight = 25529.837| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30636 Z= 0.120 Angle : 0.495 11.650 41688 Z= 0.242 Chirality : 0.034 0.171 4808 Planarity : 0.004 0.056 5264 Dihedral : 3.426 20.285 4264 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.78 % Favored : 97.11 % Rotamer: Outliers : 0.86 % Allowed : 13.48 % Favored : 85.67 % 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: 2.56 (0.14), residues: 3880 helix: 2.79 (0.10), residues: 2528 sheet: -0.95 (0.31), residues: 292 loop : -0.25 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 508 TYR 0.006 0.001 TYR B1063 PHE 0.016 0.001 PHE B 910 TRP 0.009 0.001 TRP B 772 HIS 0.004 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00271 (30632) covalent geometry : angle 0.49516 (41680) SS BOND : bond 0.00331 ( 4) SS BOND : angle 0.68497 ( 8) hydrogen bonds : bond 0.02991 ( 1916) hydrogen bonds : angle 3.93295 ( 5568) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 MET cc_start: 0.9255 (tpp) cc_final: 0.8943 (tpp) REVERT: A 599 MET cc_start: 0.8694 (ttm) cc_final: 0.8464 (ttm) REVERT: A 622 MET cc_start: 0.8502 (ttm) cc_final: 0.8094 (ttm) REVERT: A 625 ASP cc_start: 0.9027 (m-30) cc_final: 0.8736 (m-30) REVERT: B 284 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.7030 (mmt) REVERT: B 576 MET cc_start: 0.9263 (tpp) cc_final: 0.8953 (tpp) REVERT: B 599 MET cc_start: 0.8779 (ttm) cc_final: 0.8560 (ttm) REVERT: B 622 MET cc_start: 0.8493 (ttm) cc_final: 0.8070 (ttm) REVERT: B 625 ASP cc_start: 0.9029 (m-30) cc_final: 0.8739 (m-30) REVERT: C 284 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.7026 (mmt) REVERT: C 576 MET cc_start: 0.9258 (tpp) cc_final: 0.8985 (tpp) REVERT: C 599 MET cc_start: 0.8714 (ttm) cc_final: 0.8476 (ttm) REVERT: C 622 MET cc_start: 0.8495 (ttm) cc_final: 0.8134 (ttm) REVERT: C 625 ASP cc_start: 0.9034 (m-30) cc_final: 0.8739 (m-30) REVERT: D 576 MET cc_start: 0.9254 (tpp) cc_final: 0.8906 (tpp) REVERT: D 622 MET cc_start: 0.8506 (ttm) cc_final: 0.8088 (ttm) REVERT: D 625 ASP cc_start: 0.9040 (m-30) cc_final: 0.8742 (m-30) outliers start: 25 outliers final: 23 residues processed: 166 average time/residue: 0.1751 time to fit residues: 50.2164 Evaluate side-chains 173 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain D residue 20 CYS Chi-restraints excluded: chain D residue 614 ASP Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 983 MET Chi-restraints excluded: chain D residue 1034 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 124 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 267 optimal weight: 9.9990 chunk 328 optimal weight: 50.0000 chunk 103 optimal weight: 0.9990 chunk 158 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 375 optimal weight: 3.9990 chunk 371 optimal weight: 7.9990 chunk 337 optimal weight: 0.0670 chunk 38 optimal weight: 9.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.066175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.048720 restraints weight = 150628.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.050218 restraints weight = 70908.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.051255 restraints weight = 44327.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.051931 restraints weight = 32534.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.052307 restraints weight = 26434.500| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30636 Z= 0.157 Angle : 0.522 11.248 41688 Z= 0.255 Chirality : 0.035 0.165 4808 Planarity : 0.004 0.078 5264 Dihedral : 3.463 24.585 4264 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.17 % Favored : 96.73 % Rotamer: Outliers : 0.93 % Allowed : 13.61 % Favored : 85.46 % 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: 2.58 (0.14), residues: 3880 helix: 2.80 (0.11), residues: 2528 sheet: -1.04 (0.30), residues: 292 loop : -0.21 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 601 TYR 0.007 0.001 TYR A1063 PHE 0.013 0.001 PHE D 910 TRP 0.009 0.001 TRP A1124 HIS 0.002 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00353 (30632) covalent geometry : angle 0.52203 (41680) SS BOND : bond 0.00296 ( 4) SS BOND : angle 0.67618 ( 8) hydrogen bonds : bond 0.03117 ( 1916) hydrogen bonds : angle 3.99233 ( 5568) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 576 MET cc_start: 0.9242 (tpp) cc_final: 0.8886 (tpp) REVERT: A 599 MET cc_start: 0.8742 (ttm) cc_final: 0.8501 (ttm) REVERT: A 622 MET cc_start: 0.8543 (ttm) cc_final: 0.8085 (ttm) REVERT: A 625 ASP cc_start: 0.9066 (m-30) cc_final: 0.8746 (m-30) REVERT: A 988 MET cc_start: 0.8181 (mmt) cc_final: 0.7248 (mmt) REVERT: B 284 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6983 (mmt) REVERT: B 576 MET cc_start: 0.9259 (tpp) cc_final: 0.8903 (tpp) REVERT: B 599 MET cc_start: 0.8838 (ttm) cc_final: 0.8605 (ttm) REVERT: B 622 MET cc_start: 0.8546 (ttm) cc_final: 0.8080 (ttm) REVERT: B 625 ASP cc_start: 0.9064 (m-30) cc_final: 0.8749 (m-30) REVERT: C 284 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.7029 (mmt) REVERT: C 576 MET cc_start: 0.9256 (tpp) cc_final: 0.8937 (tpp) REVERT: C 599 MET cc_start: 0.8737 (ttm) cc_final: 0.8486 (ttm) REVERT: C 622 MET cc_start: 0.8539 (ttm) cc_final: 0.8115 (ttm) REVERT: C 625 ASP cc_start: 0.9058 (m-30) cc_final: 0.8741 (m-30) REVERT: C 637 ARG cc_start: 0.8216 (tmt170) cc_final: 0.7922 (ttp80) REVERT: D 576 MET cc_start: 0.9250 (tpp) cc_final: 0.8893 (tpp) REVERT: D 622 MET cc_start: 0.8535 (ttm) cc_final: 0.8077 (ttm) REVERT: D 625 ASP cc_start: 0.9060 (m-30) cc_final: 0.8744 (m-30) REVERT: D 988 MET cc_start: 0.8151 (mmt) cc_final: 0.7229 (mmt) outliers start: 27 outliers final: 24 residues processed: 157 average time/residue: 0.1809 time to fit residues: 48.7521 Evaluate side-chains 167 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 983 MET Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain D residue 20 CYS Chi-restraints excluded: chain D residue 614 ASP Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 769 LEU Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 983 MET Chi-restraints excluded: chain D residue 1034 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 266 optimal weight: 7.9990 chunk 376 optimal weight: 7.9990 chunk 163 optimal weight: 3.9990 chunk 217 optimal weight: 6.9990 chunk 154 optimal weight: 0.0370 chunk 291 optimal weight: 6.9990 chunk 201 optimal weight: 30.0000 chunk 227 optimal weight: 20.0000 chunk 211 optimal weight: 0.7980 chunk 235 optimal weight: 9.9990 chunk 223 optimal weight: 0.0970 overall best weight: 2.3860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.066344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.048709 restraints weight = 151146.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.050209 restraints weight = 70002.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.051288 restraints weight = 43536.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.052018 restraints weight = 31740.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.052449 restraints weight = 25644.104| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30636 Z= 0.133 Angle : 0.503 9.521 41688 Z= 0.247 Chirality : 0.035 0.156 4808 Planarity : 0.004 0.074 5264 Dihedral : 3.453 23.758 4264 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.89 % Favored : 97.01 % Rotamer: Outliers : 0.89 % Allowed : 13.75 % Favored : 85.36 % 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: 2.56 (0.14), residues: 3880 helix: 2.80 (0.10), residues: 2528 sheet: -1.03 (0.30), residues: 292 loop : -0.24 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 905 TYR 0.006 0.001 TYR A1063 PHE 0.012 0.001 PHE C 627 TRP 0.009 0.001 TRP C 772 HIS 0.005 0.001 HIS D 908 Details of bonding type rmsd covalent geometry : bond 0.00300 (30632) covalent geometry : angle 0.50280 (41680) SS BOND : bond 0.00302 ( 4) SS BOND : angle 0.65966 ( 8) hydrogen bonds : bond 0.03063 ( 1916) hydrogen bonds : angle 3.94964 ( 5568) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5268.53 seconds wall clock time: 91 minutes 38.05 seconds (5498.05 seconds total)