Starting phenix.real_space_refine on Wed May 28 00:44:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b92_44366/05_2025/9b92_44366.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b92_44366/05_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_44366/05_2025/9b92_44366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b92_44366/05_2025/9b92_44366.map" model { file = "/net/cci-nas-00/data/ceres_data/9b92_44366/05_2025/9b92_44366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b92_44366/05_2025/9b92_44366.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 5, 'ASP:plan': 16, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 19, 'ARG:plan': 16} 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: C, B, D Time building chain proxies: 20.53, per 1000 atoms: 0.69 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 C 35 " - pdb=" SG CYS C 37 " distance=2.97 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 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: 9.58 Conformation dependent library (CDL) restraints added in 4.3 seconds 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: 4.64 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: 11.92 Time building geometry restraints manager: 10.88 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: 0.22 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 6.730 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: 0.000 Extract box with map and model: 0.740 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 72.650 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.060 ------------------------------------------------------------------------------- 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 : 5.81 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (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 TRP 0.011 0.001 TRP A 191 HIS 0.005 0.001 HIS D 173 PHE 0.009 0.001 PHE D 899 TYR 0.010 0.001 TYR A 577 ARG 0.003 0.000 ARG B 140 Details of bonding type rmsd hydrogen bonds : bond 0.11579 ( 1916) hydrogen bonds : angle 5.56009 ( 5568) SS BOND : bond 0.94093 ( 4) SS BOND : angle 26.71579 ( 8) covalent geometry : bond 0.00589 (30632) covalent geometry : angle 0.62687 (41680) *********************** 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 : 3.333 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: 0.3894 time to fit residues: 130.7012 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 : 3.637 ------------------------------------------------------------------------------- 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 334 optimal weight: 10.0000 chunk 300 optimal weight: 8.9990 chunk 166 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 202 optimal weight: 0.9980 chunk 160 optimal weight: 9.9990 chunk 310 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 chunk 188 optimal weight: 4.9990 chunk 231 optimal weight: 20.0000 chunk 359 optimal weight: 8.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- 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 = 0.3478 r_free = 0.3478 target = 0.066268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.048405 restraints weight = 149424.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.049935 restraints weight = 69669.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.051000 restraints weight = 43095.253| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1036 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= 0.246 Angle : 0.596 6.501 41688 Z= 0.298 Chirality : 0.038 0.133 4808 Planarity : 0.004 0.036 5264 Dihedral : 4.122 55.046 4272 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.10 % Allowed : 8.71 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.14), residues: 3880 helix: 2.51 (0.10), residues: 2492 sheet: 0.41 (0.34), residues: 252 loop : -0.58 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 772 HIS 0.004 0.001 HIS B 505 PHE 0.014 0.001 PHE D 627 TYR 0.008 0.001 TYR A 211 ARG 0.003 0.000 ARG D 892 Details of bonding type rmsd hydrogen bonds : bond 0.03968 ( 1916) hydrogen bonds : angle 4.57390 ( 5568) SS BOND : bond 0.00557 ( 4) SS BOND : angle 0.69227 ( 8) covalent geometry : bond 0.00551 (30632) covalent geometry : angle 0.59581 (41680) *********************** 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 188 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 3.550 Fit side-chains REVERT: A 284 MET cc_start: 0.7089 (mtp) cc_final: 0.6803 (mmt) REVERT: A 599 MET cc_start: 0.8546 (ttp) cc_final: 0.8230 (ttm) REVERT: A 622 MET cc_start: 0.8470 (ttm) cc_final: 0.7943 (ttm) REVERT: A 625 ASP cc_start: 0.9086 (m-30) cc_final: 0.8781 (m-30) REVERT: A 926 MET cc_start: 0.9099 (mmt) cc_final: 0.8851 (mmt) REVERT: B 284 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.6959 (mmt) REVERT: B 599 MET cc_start: 0.8549 (ttp) cc_final: 0.8211 (ttm) REVERT: B 622 MET cc_start: 0.8476 (ttm) cc_final: 0.8095 (ttm) REVERT: B 625 ASP cc_start: 0.9077 (m-30) cc_final: 0.8787 (m-30) REVERT: C 284 MET cc_start: 0.7102 (mtp) cc_final: 0.6852 (mmt) REVERT: C 599 MET cc_start: 0.8550 (ttp) cc_final: 0.8216 (ttm) REVERT: C 622 MET cc_start: 0.8514 (ttm) cc_final: 0.8007 (ttm) REVERT: C 625 ASP cc_start: 0.9076 (m-30) cc_final: 0.8792 (m-30) REVERT: D 284 MET cc_start: 0.7180 (mtp) cc_final: 0.6835 (mmt) REVERT: D 599 MET cc_start: 0.8545 (ttp) cc_final: 0.8229 (ttm) REVERT: D 622 MET cc_start: 0.8476 (ttm) cc_final: 0.7918 (ttm) REVERT: D 625 ASP cc_start: 0.9080 (m-30) cc_final: 0.8783 (m-30) outliers start: 32 outliers final: 12 residues processed: 179 average time/residue: 0.3440 time to fit residues: 107.8888 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 : 3.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 614 ASP Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 1034 LEU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 315 optimal weight: 4.9990 chunk 296 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 376 optimal weight: 7.9990 chunk 65 optimal weight: 0.2980 chunk 373 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 288 optimal weight: 2.9990 chunk 102 optimal weight: 40.0000 chunk 125 optimal weight: 6.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.067172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.049253 restraints weight = 147740.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.050847 restraints weight = 66872.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.051967 restraints weight = 40746.159| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30636 Z= 0.136 Angle : 0.482 7.074 41688 Z= 0.245 Chirality : 0.035 0.131 4808 Planarity : 0.004 0.042 5264 Dihedral : 3.669 23.448 4264 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.65 % Allowed : 10.53 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.14), residues: 3880 helix: 2.69 (0.11), residues: 2496 sheet: 1.00 (0.39), residues: 208 loop : -0.62 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 772 HIS 0.002 0.001 HIS D 505 PHE 0.015 0.001 PHE C 627 TYR 0.006 0.001 TYR A 211 ARG 0.004 0.000 ARG D 459 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 1916) hydrogen bonds : angle 4.19830 ( 5568) SS BOND : bond 0.00221 ( 4) SS BOND : angle 0.53120 ( 8) covalent geometry : bond 0.00304 (30632) covalent geometry : angle 0.48195 (41680) *********************** 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 181 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 3.414 Fit side-chains REVERT: A 284 MET cc_start: 0.7346 (mtp) cc_final: 0.6912 (mmt) REVERT: A 599 MET cc_start: 0.8541 (ttp) cc_final: 0.8236 (ttm) REVERT: A 622 MET cc_start: 0.8421 (ttm) cc_final: 0.8041 (ttm) REVERT: A 625 ASP cc_start: 0.9068 (m-30) cc_final: 0.8784 (m-30) REVERT: B 284 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.6950 (mmt) REVERT: B 599 MET cc_start: 0.8570 (ttp) cc_final: 0.8255 (ttm) REVERT: B 622 MET cc_start: 0.8410 (ttm) cc_final: 0.8040 (ttm) REVERT: B 625 ASP cc_start: 0.9076 (m-30) cc_final: 0.8797 (m-30) REVERT: C 284 MET cc_start: 0.7345 (mtp) cc_final: 0.6977 (mmt) REVERT: C 599 MET cc_start: 0.8545 (ttp) cc_final: 0.8241 (ttm) REVERT: C 622 MET cc_start: 0.8432 (ttm) cc_final: 0.8064 (ttm) REVERT: C 625 ASP cc_start: 0.9075 (m-30) cc_final: 0.8771 (m-30) REVERT: D 284 MET cc_start: 0.7333 (mtp) cc_final: 0.6894 (mmt) REVERT: D 599 MET cc_start: 0.8542 (ttp) cc_final: 0.8236 (ttm) REVERT: D 622 MET cc_start: 0.8434 (ttm) cc_final: 0.8054 (ttm) REVERT: D 625 ASP cc_start: 0.9077 (m-30) cc_final: 0.8772 (m-30) outliers start: 19 outliers final: 7 residues processed: 170 average time/residue: 0.3792 time to fit residues: 110.1545 Evaluate side-chains 156 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 148 time to evaluate : 3.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain D residue 614 ASP 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 354 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 228 optimal weight: 20.0000 chunk 56 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 120 optimal weight: 30.0000 chunk 235 optimal weight: 0.7980 chunk 150 optimal weight: 30.0000 chunk 171 optimal weight: 10.0000 chunk 320 optimal weight: 10.0000 chunk 210 optimal weight: 9.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 669 GLN ** A1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 HIS ** B 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN B 669 GLN B1084 HIS ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 GLN C 669 GLN ** C1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1084 HIS ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 GLN D1084 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.065293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.047344 restraints weight = 150248.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.048835 restraints weight = 70681.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.049875 restraints weight = 44095.768| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 30636 Z= 0.270 Angle : 0.625 7.869 41688 Z= 0.303 Chirality : 0.038 0.124 4808 Planarity : 0.004 0.045 5264 Dihedral : 3.802 25.014 4264 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.54 % Allowed : 11.39 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.14), residues: 3880 helix: 2.53 (0.10), residues: 2492 sheet: -0.19 (0.32), residues: 276 loop : -0.50 (0.19), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1124 HIS 0.004 0.001 HIS A 173 PHE 0.016 0.001 PHE D 910 TYR 0.011 0.001 TYR A 577 ARG 0.004 0.000 ARG A1138 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 1916) hydrogen bonds : angle 4.38159 ( 5568) SS BOND : bond 0.00197 ( 4) SS BOND : angle 0.84544 ( 8) covalent geometry : bond 0.00599 (30632) covalent geometry : angle 0.62502 (41680) *********************** 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 189 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 144 time to evaluate : 3.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.6783 (mmt) REVERT: A 599 MET cc_start: 0.8664 (ttp) cc_final: 0.8464 (ttm) REVERT: A 622 MET cc_start: 0.8576 (ttm) cc_final: 0.8276 (ttm) REVERT: A 625 ASP cc_start: 0.9082 (m-30) cc_final: 0.8781 (m-30) REVERT: B 284 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.6844 (mmt) REVERT: B 599 MET cc_start: 0.8718 (ttp) cc_final: 0.8504 (ttm) REVERT: B 622 MET cc_start: 0.8548 (ttm) cc_final: 0.8222 (ttm) REVERT: B 625 ASP cc_start: 0.9071 (m-30) cc_final: 0.8782 (m-30) REVERT: B 927 MET cc_start: 0.8421 (mmt) cc_final: 0.8019 (mmt) REVERT: C 284 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.6966 (mmt) REVERT: C 599 MET cc_start: 0.8695 (ttp) cc_final: 0.8486 (ttm) REVERT: C 622 MET cc_start: 0.8573 (ttm) cc_final: 0.8111 (ttm) REVERT: C 625 ASP cc_start: 0.9088 (m-30) cc_final: 0.8789 (m-30) REVERT: D 284 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.6880 (mmt) REVERT: D 599 MET cc_start: 0.8698 (ttp) cc_final: 0.8484 (ttm) REVERT: D 622 MET cc_start: 0.8576 (ttm) cc_final: 0.8276 (ttm) REVERT: D 625 ASP cc_start: 0.9085 (m-30) cc_final: 0.8782 (m-30) outliers start: 45 outliers final: 24 residues processed: 170 average time/residue: 0.3707 time to fit residues: 108.1755 Evaluate side-chains 173 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 3.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 284 MET 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 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 800 VAL 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 20 CYS Chi-restraints excluded: chain C residue 109 THR 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 1034 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 284 MET 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 1034 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 370 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 271 optimal weight: 0.9990 chunk 303 optimal weight: 20.0000 chunk 380 optimal weight: 7.9990 chunk 294 optimal weight: 9.9990 chunk 385 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 199 optimal weight: 7.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** A1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN ** C1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.067016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.049063 restraints weight = 146812.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.050621 restraints weight = 67008.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.051719 restraints weight = 41306.682| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 30636 Z= 0.101 Angle : 0.469 6.807 41688 Z= 0.238 Chirality : 0.034 0.122 4808 Planarity : 0.004 0.047 5264 Dihedral : 3.658 22.043 4264 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.10 % Allowed : 11.93 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.14), residues: 3880 helix: 2.71 (0.10), residues: 2500 sheet: -0.54 (0.34), residues: 276 loop : -0.34 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 772 HIS 0.005 0.001 HIS A1002 PHE 0.015 0.001 PHE C 627 TYR 0.006 0.001 TYR C 211 ARG 0.002 0.000 ARG C1138 Details of bonding type rmsd hydrogen bonds : bond 0.03261 ( 1916) hydrogen bonds : angle 4.02901 ( 5568) SS BOND : bond 0.00332 ( 4) SS BOND : angle 0.71404 ( 8) covalent geometry : bond 0.00219 (30632) covalent geometry : angle 0.46875 (41680) *********************** 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 186 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 3.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.6995 (mmt) REVERT: A 576 MET cc_start: 0.9221 (tpp) cc_final: 0.8938 (tpp) REVERT: A 581 MET cc_start: 0.8861 (mmm) cc_final: 0.8600 (mmp) REVERT: A 599 MET cc_start: 0.8642 (ttp) cc_final: 0.8316 (ttm) REVERT: A 622 MET cc_start: 0.8462 (ttm) cc_final: 0.8067 (ttm) REVERT: A 625 ASP cc_start: 0.9036 (m-30) cc_final: 0.8765 (m-30) REVERT: B 284 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.6944 (mmt) REVERT: B 576 MET cc_start: 0.9250 (tpp) cc_final: 0.8962 (tpp) REVERT: B 599 MET cc_start: 0.8668 (ttp) cc_final: 0.8319 (ttm) REVERT: B 622 MET cc_start: 0.8458 (ttm) cc_final: 0.8061 (ttm) REVERT: B 625 ASP cc_start: 0.9012 (m-30) cc_final: 0.8719 (m-30) REVERT: C 284 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.7048 (mmt) REVERT: C 576 MET cc_start: 0.9245 (tpp) cc_final: 0.8993 (tpp) REVERT: C 581 MET cc_start: 0.8837 (mmm) cc_final: 0.8583 (mmp) REVERT: C 599 MET cc_start: 0.8656 (ttp) cc_final: 0.8324 (ttm) REVERT: C 622 MET cc_start: 0.8450 (ttm) cc_final: 0.8127 (ttm) REVERT: C 625 ASP cc_start: 0.9020 (m-30) cc_final: 0.8744 (m-30) REVERT: D 284 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.7042 (mmt) REVERT: D 576 MET cc_start: 0.9225 (tpp) cc_final: 0.8902 (tpp) REVERT: D 581 MET cc_start: 0.8858 (mmm) cc_final: 0.8607 (mmp) REVERT: D 599 MET cc_start: 0.8653 (ttp) cc_final: 0.8307 (ttm) REVERT: D 622 MET cc_start: 0.8467 (ttm) cc_final: 0.8056 (ttm) REVERT: D 625 ASP cc_start: 0.9025 (m-30) cc_final: 0.8745 (m-30) outliers start: 32 outliers final: 17 residues processed: 167 average time/residue: 0.3815 time to fit residues: 110.1932 Evaluate side-chains 158 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 3.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 614 ASP 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 20 CYS Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain D residue 20 CYS Chi-restraints excluded: chain D residue 284 MET 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 134 optimal weight: 8.9990 chunk 170 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 394 optimal weight: 1.9990 chunk 245 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 153 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 232 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 chunk 357 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.065028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.047033 restraints weight = 151152.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.048516 restraints weight = 70584.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.049494 restraints weight = 43401.480| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 30636 Z= 0.261 Angle : 0.608 7.154 41688 Z= 0.294 Chirality : 0.037 0.122 4808 Planarity : 0.004 0.048 5264 Dihedral : 3.735 24.252 4264 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.34 % Allowed : 12.93 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.14), residues: 3880 helix: 2.65 (0.11), residues: 2500 sheet: -0.76 (0.32), residues: 272 loop : -0.31 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D1124 HIS 0.004 0.001 HIS B1002 PHE 0.016 0.001 PHE B 910 TYR 0.011 0.001 TYR D 577 ARG 0.003 0.000 ARG D 892 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 1916) hydrogen bonds : angle 4.24957 ( 5568) SS BOND : bond 0.00199 ( 4) SS BOND : angle 0.80811 ( 8) covalent geometry : bond 0.00578 (30632) covalent geometry : angle 0.60824 (41680) *********************** 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 171 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 132 time to evaluate : 3.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.6991 (mmt) REVERT: A 581 MET cc_start: 0.8996 (mmm) cc_final: 0.8768 (mmp) REVERT: A 599 MET cc_start: 0.8765 (ttp) cc_final: 0.8418 (ttp) REVERT: A 622 MET cc_start: 0.8583 (ttm) cc_final: 0.8098 (ttm) REVERT: A 625 ASP cc_start: 0.9060 (m-30) cc_final: 0.8743 (m-30) REVERT: B 284 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.6858 (mmt) REVERT: B 576 MET cc_start: 0.9250 (tpp) cc_final: 0.8887 (tpp) REVERT: B 584 ASN cc_start: 0.8948 (OUTLIER) cc_final: 0.8737 (p0) REVERT: B 599 MET cc_start: 0.8751 (ttp) cc_final: 0.8444 (ttp) REVERT: B 622 MET cc_start: 0.8587 (ttm) cc_final: 0.8069 (ttm) REVERT: B 625 ASP cc_start: 0.9061 (m-30) cc_final: 0.8751 (m-30) REVERT: B 927 MET cc_start: 0.8424 (mmt) cc_final: 0.8103 (mmp) REVERT: B 988 MET cc_start: 0.7873 (mtp) cc_final: 0.7345 (mtp) REVERT: C 284 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6984 (mmt) REVERT: C 576 MET cc_start: 0.9209 (tpp) cc_final: 0.8890 (tpp) REVERT: C 581 MET cc_start: 0.8970 (mmm) cc_final: 0.8746 (mmp) REVERT: C 584 ASN cc_start: 0.8933 (OUTLIER) cc_final: 0.8713 (p0) REVERT: C 599 MET cc_start: 0.8736 (ttp) cc_final: 0.8473 (ttm) REVERT: C 622 MET cc_start: 0.8613 (ttm) cc_final: 0.8145 (ttm) REVERT: C 625 ASP cc_start: 0.9068 (m-30) cc_final: 0.8756 (m-30) REVERT: C 988 MET cc_start: 0.7827 (mtp) cc_final: 0.7318 (mtp) REVERT: D 284 MET cc_start: 0.7420 (OUTLIER) cc_final: 0.6974 (mmt) REVERT: D 576 MET cc_start: 0.9250 (tpp) cc_final: 0.8889 (tpp) REVERT: D 581 MET cc_start: 0.8984 (mmm) cc_final: 0.8755 (mmp) REVERT: D 599 MET cc_start: 0.8785 (ttp) cc_final: 0.8431 (ttp) REVERT: D 622 MET cc_start: 0.8584 (ttm) cc_final: 0.8063 (ttm) REVERT: D 625 ASP cc_start: 0.9071 (m-30) cc_final: 0.8775 (m-30) REVERT: D 988 MET cc_start: 0.7835 (mtp) cc_final: 0.7317 (mtp) outliers start: 39 outliers final: 29 residues processed: 160 average time/residue: 0.3702 time to fit residues: 101.7501 Evaluate side-chains 169 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 3.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 MET 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 A residue 983 MET 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 584 ASN 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 1035 LEU Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 584 ASN 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 1035 LEU Chi-restraints excluded: chain C residue 1156 ASP Chi-restraints excluded: chain D residue 20 CYS Chi-restraints excluded: chain D residue 284 MET 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 1035 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 368 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 291 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 342 optimal weight: 0.0980 chunk 289 optimal weight: 2.9990 chunk 207 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 266 optimal weight: 0.0970 chunk 232 optimal weight: 0.4980 chunk 286 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1037 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 = 0.3499 r_free = 0.3499 target = 0.067149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.049287 restraints weight = 146871.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.050847 restraints weight = 67132.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.051898 restraints weight = 41178.282| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 30636 Z= 0.095 Angle : 0.466 7.114 41688 Z= 0.235 Chirality : 0.034 0.120 4808 Planarity : 0.004 0.048 5264 Dihedral : 3.586 20.777 4264 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.75 % Allowed : 14.13 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.14), residues: 3880 helix: 2.80 (0.10), residues: 2500 sheet: -0.81 (0.32), residues: 280 loop : -0.34 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 772 HIS 0.002 0.001 HIS B 424 PHE 0.015 0.001 PHE A 627 TYR 0.005 0.001 TYR A 211 ARG 0.002 0.000 ARG B 327 Details of bonding type rmsd hydrogen bonds : bond 0.03113 ( 1916) hydrogen bonds : angle 3.93959 ( 5568) SS BOND : bond 0.00338 ( 4) SS BOND : angle 0.74171 ( 8) covalent geometry : bond 0.00202 (30632) covalent geometry : angle 0.46631 (41680) *********************** 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 175 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 3.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.7042 (mmt) REVERT: A 576 MET cc_start: 0.9262 (tpp) cc_final: 0.8952 (tpp) REVERT: A 581 MET cc_start: 0.8961 (mmm) cc_final: 0.8710 (mmp) REVERT: A 622 MET cc_start: 0.8554 (ttm) cc_final: 0.8165 (ttm) REVERT: A 625 ASP cc_start: 0.9048 (m-30) cc_final: 0.8745 (m-30) REVERT: B 284 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.6925 (mmt) REVERT: B 576 MET cc_start: 0.9297 (tpp) cc_final: 0.8990 (tpp) REVERT: B 599 MET cc_start: 0.8787 (ttp) cc_final: 0.8573 (ttm) REVERT: B 622 MET cc_start: 0.8533 (ttm) cc_final: 0.8149 (ttm) REVERT: B 625 ASP cc_start: 0.9047 (m-30) cc_final: 0.8744 (m-30) REVERT: C 284 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.6952 (mmt) REVERT: C 576 MET cc_start: 0.9294 (tpp) cc_final: 0.9029 (tpp) REVERT: C 581 MET cc_start: 0.8942 (mmm) cc_final: 0.8693 (mmp) REVERT: C 599 MET cc_start: 0.8779 (ttp) cc_final: 0.8567 (ttm) REVERT: C 622 MET cc_start: 0.8529 (ttm) cc_final: 0.8176 (ttm) REVERT: C 625 ASP cc_start: 0.9043 (m-30) cc_final: 0.8741 (m-30) REVERT: D 284 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.7034 (mmt) REVERT: D 576 MET cc_start: 0.9264 (tpp) cc_final: 0.8955 (tpp) REVERT: D 581 MET cc_start: 0.8961 (mmm) cc_final: 0.8711 (mmp) REVERT: D 622 MET cc_start: 0.8518 (ttm) cc_final: 0.8135 (ttm) REVERT: D 625 ASP cc_start: 0.9054 (m-30) cc_final: 0.8741 (m-30) outliers start: 22 outliers final: 15 residues processed: 165 average time/residue: 0.3849 time to fit residues: 107.9152 Evaluate side-chains 163 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 3.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 707 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 912 VAL Chi-restraints excluded: chain B residue 1156 ASP Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 1156 ASP Chi-restraints excluded: chain D residue 20 CYS Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 614 ASP Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 912 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 78 optimal weight: 2.9990 chunk 133 optimal weight: 20.0000 chunk 254 optimal weight: 3.9990 chunk 231 optimal weight: 0.0060 chunk 46 optimal weight: 10.0000 chunk 297 optimal weight: 6.9990 chunk 295 optimal weight: 0.7980 chunk 104 optimal weight: 20.0000 chunk 307 optimal weight: 30.0000 chunk 92 optimal weight: 10.0000 chunk 287 optimal weight: 7.9990 overall best weight: 2.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.066356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.048589 restraints weight = 150976.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.050099 restraints weight = 70484.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.051136 restraints weight = 43583.877| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30636 Z= 0.156 Angle : 0.506 7.112 41688 Z= 0.251 Chirality : 0.034 0.117 4808 Planarity : 0.004 0.047 5264 Dihedral : 3.526 21.615 4264 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.22 % Favored : 96.68 % Rotamer: Outliers : 0.93 % Allowed : 13.79 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.14), residues: 3880 helix: 2.83 (0.11), residues: 2504 sheet: -0.87 (0.31), residues: 280 loop : -0.24 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 772 HIS 0.004 0.001 HIS A 505 PHE 0.015 0.001 PHE C 910 TYR 0.006 0.001 TYR A 464 ARG 0.004 0.000 ARG B1138 Details of bonding type rmsd hydrogen bonds : bond 0.03138 ( 1916) hydrogen bonds : angle 4.02853 ( 5568) SS BOND : bond 0.00312 ( 4) SS BOND : angle 0.71603 ( 8) covalent geometry : bond 0.00351 (30632) covalent geometry : angle 0.50557 (41680) *********************** 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 168 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 3.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.6964 (mmt) REVERT: A 576 MET cc_start: 0.9255 (tpp) cc_final: 0.8941 (tpp) REVERT: A 581 MET cc_start: 0.8995 (mmm) cc_final: 0.8750 (mmp) REVERT: A 599 MET cc_start: 0.8734 (ttm) cc_final: 0.8500 (ttm) REVERT: A 622 MET cc_start: 0.8548 (ttm) cc_final: 0.8120 (ttm) REVERT: A 625 ASP cc_start: 0.9049 (m-30) cc_final: 0.8748 (m-30) REVERT: B 284 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.6996 (mmt) REVERT: B 576 MET cc_start: 0.9279 (tpp) cc_final: 0.8954 (tpp) REVERT: B 599 MET cc_start: 0.8788 (ttp) cc_final: 0.8485 (ttp) REVERT: B 622 MET cc_start: 0.8539 (ttm) cc_final: 0.8109 (ttm) REVERT: B 625 ASP cc_start: 0.9048 (m-30) cc_final: 0.8741 (m-30) REVERT: C 284 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.7047 (mmt) REVERT: C 576 MET cc_start: 0.9258 (tpp) cc_final: 0.8987 (tpp) REVERT: C 581 MET cc_start: 0.8967 (mmm) cc_final: 0.8729 (mmp) REVERT: C 599 MET cc_start: 0.8816 (ttp) cc_final: 0.8508 (ttp) REVERT: C 622 MET cc_start: 0.8537 (ttm) cc_final: 0.8156 (ttm) REVERT: C 625 ASP cc_start: 0.9042 (m-30) cc_final: 0.8739 (m-30) REVERT: D 284 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.7000 (mmt) REVERT: D 576 MET cc_start: 0.9267 (tpp) cc_final: 0.8912 (tpp) REVERT: D 581 MET cc_start: 0.8977 (mmm) cc_final: 0.8735 (mmp) REVERT: D 599 MET cc_start: 0.8734 (ttm) cc_final: 0.8506 (ttm) REVERT: D 622 MET cc_start: 0.8540 (ttm) cc_final: 0.8075 (ttm) REVERT: D 625 ASP cc_start: 0.9039 (m-30) cc_final: 0.8741 (m-30) outliers start: 27 outliers final: 22 residues processed: 158 average time/residue: 0.3652 time to fit residues: 99.4553 Evaluate side-chains 166 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 3.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 284 MET 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 1156 ASP Chi-restraints excluded: chain C residue 20 CYS 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 912 VAL Chi-restraints excluded: chain C residue 1156 ASP Chi-restraints excluded: chain D residue 20 CYS Chi-restraints excluded: chain D residue 284 MET 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 218 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 244 optimal weight: 9.9990 chunk 293 optimal weight: 6.9990 chunk 319 optimal weight: 8.9990 chunk 300 optimal weight: 30.0000 chunk 364 optimal weight: 0.9980 chunk 284 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 186 optimal weight: 0.8980 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.065719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.047665 restraints weight = 150067.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.049182 restraints weight = 70329.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.050250 restraints weight = 43901.723| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2166 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= 0.181 Angle : 0.535 7.791 41688 Z= 0.264 Chirality : 0.035 0.151 4808 Planarity : 0.004 0.048 5264 Dihedral : 3.565 22.567 4264 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.40 % Favored : 96.49 % Rotamer: Outliers : 1.06 % Allowed : 13.96 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.14), residues: 3880 helix: 2.80 (0.10), residues: 2512 sheet: -0.95 (0.31), residues: 280 loop : -0.29 (0.19), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1124 HIS 0.009 0.001 HIS D 505 PHE 0.018 0.001 PHE D 910 TYR 0.007 0.001 TYR D1063 ARG 0.007 0.000 ARG D 508 Details of bonding type rmsd hydrogen bonds : bond 0.03269 ( 1916) hydrogen bonds : angle 4.10493 ( 5568) SS BOND : bond 0.00270 ( 4) SS BOND : angle 0.71966 ( 8) covalent geometry : bond 0.00405 (30632) covalent geometry : angle 0.53541 (41680) *********************** 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 169 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 3.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.6998 (mmt) REVERT: A 576 MET cc_start: 0.9201 (tpp) cc_final: 0.8844 (tpp) REVERT: A 581 MET cc_start: 0.8948 (mmm) cc_final: 0.8719 (mmp) REVERT: A 599 MET cc_start: 0.8792 (ttm) cc_final: 0.8562 (ttm) REVERT: A 622 MET cc_start: 0.8531 (ttm) cc_final: 0.8091 (ttm) REVERT: A 625 ASP cc_start: 0.9004 (m-30) cc_final: 0.8706 (m-30) REVERT: B 284 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.7021 (mmt) REVERT: B 576 MET cc_start: 0.9248 (tpp) cc_final: 0.8871 (tpp) REVERT: B 622 MET cc_start: 0.8527 (ttm) cc_final: 0.8091 (ttm) REVERT: B 625 ASP cc_start: 0.9011 (m-30) cc_final: 0.8711 (m-30) REVERT: C 284 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.7048 (mmt) REVERT: C 576 MET cc_start: 0.9221 (tpp) cc_final: 0.8901 (tpp) REVERT: C 581 MET cc_start: 0.8936 (mmm) cc_final: 0.8711 (mmp) REVERT: C 622 MET cc_start: 0.8538 (ttm) cc_final: 0.8131 (ttm) REVERT: C 625 ASP cc_start: 0.8999 (m-30) cc_final: 0.8708 (m-30) REVERT: D 284 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.7002 (mmt) REVERT: D 576 MET cc_start: 0.9221 (tpp) cc_final: 0.8858 (tpp) REVERT: D 581 MET cc_start: 0.8943 (mmm) cc_final: 0.8717 (mmp) REVERT: D 599 MET cc_start: 0.8797 (ttm) cc_final: 0.8576 (ttm) REVERT: D 622 MET cc_start: 0.8528 (ttm) cc_final: 0.8054 (ttm) REVERT: D 625 ASP cc_start: 0.8999 (m-30) cc_final: 0.8704 (m-30) outliers start: 31 outliers final: 22 residues processed: 161 average time/residue: 0.3787 time to fit residues: 104.9541 Evaluate side-chains 161 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 3.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 284 MET 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 1156 ASP Chi-restraints excluded: chain C residue 20 CYS 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 912 VAL Chi-restraints excluded: chain C residue 1156 ASP Chi-restraints excluded: chain D residue 20 CYS Chi-restraints excluded: chain D residue 284 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 343 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 338 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 311 optimal weight: 20.0000 chunk 375 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 340 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.3479 r_free = 0.3479 target = 0.066028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.048439 restraints weight = 150764.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.049896 restraints weight = 69454.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.050978 restraints weight = 43331.424| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30636 Z= 0.127 Angle : 0.505 9.831 41688 Z= 0.253 Chirality : 0.035 0.163 4808 Planarity : 0.004 0.048 5264 Dihedral : 3.530 21.638 4264 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.99 % Favored : 96.91 % Rotamer: Outliers : 0.86 % Allowed : 14.37 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.14), residues: 3880 helix: 2.78 (0.10), residues: 2524 sheet: -0.86 (0.32), residues: 276 loop : -0.29 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 772 HIS 0.002 0.000 HIS B 505 PHE 0.016 0.001 PHE C 910 TYR 0.006 0.001 TYR B1063 ARG 0.004 0.000 ARG C 612 Details of bonding type rmsd hydrogen bonds : bond 0.03207 ( 1916) hydrogen bonds : angle 4.03227 ( 5568) SS BOND : bond 0.00302 ( 4) SS BOND : angle 0.68878 ( 8) covalent geometry : bond 0.00287 (30632) covalent geometry : angle 0.50518 (41680) ********************** 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 163 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 3.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.7022 (mmt) REVERT: A 576 MET cc_start: 0.9229 (tpp) cc_final: 0.8910 (tpp) REVERT: A 581 MET cc_start: 0.8965 (mmm) cc_final: 0.8725 (mmp) REVERT: A 599 MET cc_start: 0.8812 (ttm) cc_final: 0.8584 (ttm) REVERT: A 622 MET cc_start: 0.8547 (ttm) cc_final: 0.8101 (ttm) REVERT: A 625 ASP cc_start: 0.9055 (m-30) cc_final: 0.8743 (m-30) REVERT: A 988 MET cc_start: 0.8218 (mmt) cc_final: 0.7366 (mmt) REVERT: B 284 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.6990 (mmt) REVERT: B 576 MET cc_start: 0.9274 (tpp) cc_final: 0.8936 (tpp) REVERT: B 599 MET cc_start: 0.8916 (ttp) cc_final: 0.8608 (ttp) REVERT: B 622 MET cc_start: 0.8546 (ttm) cc_final: 0.8098 (ttm) REVERT: B 625 ASP cc_start: 0.9059 (m-30) cc_final: 0.8748 (m-30) REVERT: C 284 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.7051 (mmt) REVERT: C 576 MET cc_start: 0.9267 (tpp) cc_final: 0.8975 (tpp) REVERT: C 581 MET cc_start: 0.8961 (mmm) cc_final: 0.8710 (mmp) REVERT: C 599 MET cc_start: 0.8830 (ttm) cc_final: 0.8456 (ttm) REVERT: C 622 MET cc_start: 0.8560 (ttm) cc_final: 0.8159 (ttm) REVERT: C 625 ASP cc_start: 0.9061 (m-30) cc_final: 0.8752 (m-30) REVERT: D 284 MET cc_start: 0.7438 (OUTLIER) cc_final: 0.7080 (mmt) REVERT: D 576 MET cc_start: 0.9246 (tpp) cc_final: 0.8880 (tpp) REVERT: D 581 MET cc_start: 0.8959 (mmm) cc_final: 0.8721 (mmp) REVERT: D 599 MET cc_start: 0.8799 (ttm) cc_final: 0.8576 (ttm) REVERT: D 622 MET cc_start: 0.8559 (ttm) cc_final: 0.8114 (ttm) REVERT: D 625 ASP cc_start: 0.9044 (m-30) cc_final: 0.8731 (m-30) outliers start: 25 outliers final: 19 residues processed: 153 average time/residue: 0.3698 time to fit residues: 97.8726 Evaluate side-chains 161 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 3.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 707 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 1156 ASP Chi-restraints excluded: chain C residue 20 CYS 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 912 VAL Chi-restraints excluded: chain C residue 1156 ASP Chi-restraints excluded: chain D residue 20 CYS Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 614 ASP Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 912 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 274 optimal weight: 8.9990 chunk 366 optimal weight: 9.9990 chunk 104 optimal weight: 20.0000 chunk 85 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 261 optimal weight: 5.9990 chunk 278 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 260 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 505 HIS ** 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 = 0.3472 r_free = 0.3472 target = 0.065747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.048111 restraints weight = 151328.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.049625 restraints weight = 70409.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.050664 restraints weight = 43708.432| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30636 Z= 0.150 Angle : 0.520 9.673 41688 Z= 0.259 Chirality : 0.035 0.169 4808 Planarity : 0.004 0.048 5264 Dihedral : 3.517 21.865 4264 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.38 % Favored : 96.52 % Rotamer: Outliers : 0.89 % Allowed : 14.33 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.14), residues: 3880 helix: 2.79 (0.10), residues: 2524 sheet: -0.92 (0.31), residues: 276 loop : -0.28 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 772 HIS 0.002 0.001 HIS D 505 PHE 0.014 0.001 PHE A 910 TYR 0.007 0.001 TYR D1063 ARG 0.004 0.000 ARG C 612 Details of bonding type rmsd hydrogen bonds : bond 0.03228 ( 1916) hydrogen bonds : angle 4.04354 ( 5568) SS BOND : bond 0.00287 ( 4) SS BOND : angle 0.70291 ( 8) covalent geometry : bond 0.00339 (30632) covalent geometry : angle 0.52003 (41680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9097.68 seconds wall clock time: 160 minutes 2.17 seconds (9602.17 seconds total)