Starting phenix.real_space_refine on Thu Jun 26 02:10:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b92_44366/06_2025/9b92_44366.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b92_44366/06_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_44366/06_2025/9b92_44366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b92_44366/06_2025/9b92_44366.map" model { file = "/net/cci-nas-00/data/ceres_data/9b92_44366/06_2025/9b92_44366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b92_44366/06_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-5710/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: 21.26, per 1000 atoms: 0.71 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: 8.19 Conformation dependent library (CDL) restraints added in 3.9 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: 3.80 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: 13.05 Time building geometry restraints manager: 9.59 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: 4.340 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: 0.040 Extract box with map and model: 1.400 Check model and map are aligned: 0.270 Set scattering table: 0.310 Process input model: 74.040 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.080 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.260 ------------------------------------------------------------------------------- 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 : 4.204 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: 0.3939 time to fit residues: 132.6591 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 : 3.180 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.066265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.048447 restraints weight = 149498.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.049959 restraints weight = 69305.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.051021 restraints weight = 42637.662| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- 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 55.047 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 4.57391 ( 5568) SS BOND : bond 0.00558 ( 4) SS BOND : angle 0.69218 ( 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 : 3.150 Fit side-chains REVERT: A 284 MET cc_start: 0.7088 (mtp) cc_final: 0.6801 (mmt) REVERT: A 599 MET cc_start: 0.8547 (ttp) cc_final: 0.8230 (ttm) REVERT: A 622 MET cc_start: 0.8469 (ttm) cc_final: 0.7939 (ttm) REVERT: A 625 ASP cc_start: 0.9087 (m-30) cc_final: 0.8782 (m-30) REVERT: A 926 MET cc_start: 0.9099 (mmt) cc_final: 0.8852 (mmt) REVERT: B 284 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.6961 (mmt) REVERT: B 599 MET cc_start: 0.8550 (ttp) cc_final: 0.8212 (ttm) REVERT: B 622 MET cc_start: 0.8476 (ttm) cc_final: 0.8095 (ttm) REVERT: B 625 ASP cc_start: 0.9079 (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: 0.8551 (ttp) cc_final: 0.8217 (ttm) REVERT: C 622 MET cc_start: 0.8514 (ttm) cc_final: 0.8006 (ttm) REVERT: C 625 ASP cc_start: 0.9076 (m-30) cc_final: 0.8792 (m-30) REVERT: D 284 MET cc_start: 0.7181 (mtp) cc_final: 0.6835 (mmt) REVERT: D 599 MET cc_start: 0.8546 (ttp) cc_final: 0.8230 (ttm) REVERT: D 622 MET cc_start: 0.8474 (ttm) cc_final: 0.7915 (ttm) REVERT: D 625 ASP cc_start: 0.9081 (m-30) cc_final: 0.8784 (m-30) outliers start: 32 outliers final: 12 residues processed: 179 average time/residue: 0.3507 time to fit residues: 110.0903 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 : 3.118 ------------------------------------------------------------------------------- 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: 0.7980 chunk 296 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 376 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 373 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 134 optimal weight: 9.9990 chunk 288 optimal weight: 3.9990 chunk 102 optimal weight: 40.0000 chunk 125 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.067451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.049378 restraints weight = 147072.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.050955 restraints weight = 67111.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.052070 restraints weight = 41201.639| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 30636 Z= 0.114 Angle : 0.470 7.325 41688 Z= 0.240 Chirality : 0.035 0.132 4808 Planarity : 0.004 0.041 5264 Dihedral : 3.646 22.939 4264 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.51 % Allowed : 10.43 % Favored : 89.06 % 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: 2.51 (0.14), residues: 3880 helix: 2.71 (0.11), residues: 2496 sheet: 1.17 (0.40), residues: 200 loop : -0.62 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 772 HIS 0.002 0.000 HIS B 424 PHE 0.014 0.001 PHE C 627 TYR 0.006 0.001 TYR A 211 ARG 0.004 0.000 ARG A 459 Details of bonding type rmsd hydrogen bonds : bond 0.03403 ( 1916) hydrogen bonds : angle 4.15386 ( 5568) SS BOND : bond 0.00480 ( 4) SS BOND : angle 0.49477 ( 8) covalent geometry : bond 0.00250 (30632) covalent geometry : angle 0.47043 (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 186 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 3.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 MET cc_start: 0.7327 (mtp) cc_final: 0.6898 (mmt) REVERT: A 599 MET cc_start: 0.8507 (ttp) cc_final: 0.8180 (ttm) REVERT: A 622 MET cc_start: 0.8445 (ttm) cc_final: 0.8067 (ttm) REVERT: A 625 ASP cc_start: 0.9102 (m-30) cc_final: 0.8807 (m-30) REVERT: B 284 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6992 (mmt) REVERT: B 599 MET cc_start: 0.8541 (ttp) cc_final: 0.8227 (ttm) REVERT: B 622 MET cc_start: 0.8442 (ttm) cc_final: 0.8069 (ttm) REVERT: B 625 ASP cc_start: 0.9109 (m-30) cc_final: 0.8819 (m-30) REVERT: C 284 MET cc_start: 0.7310 (mtp) cc_final: 0.6954 (mmt) REVERT: C 599 MET cc_start: 0.8526 (ttp) cc_final: 0.8205 (ttm) REVERT: C 622 MET cc_start: 0.8444 (ttm) cc_final: 0.8054 (ttm) REVERT: C 625 ASP cc_start: 0.9097 (m-30) cc_final: 0.8793 (m-30) REVERT: D 284 MET cc_start: 0.7362 (mtp) cc_final: 0.6937 (mmt) REVERT: D 599 MET cc_start: 0.8539 (ttp) cc_final: 0.8225 (ttm) REVERT: D 622 MET cc_start: 0.8440 (ttm) cc_final: 0.8066 (ttm) REVERT: D 625 ASP cc_start: 0.9104 (m-30) cc_final: 0.8815 (m-30) outliers start: 15 outliers final: 7 residues processed: 175 average time/residue: 0.4611 time to fit residues: 137.6583 Evaluate side-chains 163 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 155 time to evaluate : 4.208 ------------------------------------------------------------------------------- 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: 7.9990 chunk 11 optimal weight: 9.9990 chunk 228 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 120 optimal weight: 30.0000 chunk 235 optimal weight: 0.8980 chunk 150 optimal weight: 0.0970 chunk 171 optimal weight: 10.0000 chunk 320 optimal weight: 10.0000 chunk 210 optimal weight: 9.9990 overall best weight: 4.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 669 GLN ** A1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 HIS B 116 ASN B 669 GLN ** B1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1084 HIS C 116 ASN 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 ** D1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1084 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.065663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.047581 restraints weight = 149727.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.049056 restraints weight = 70394.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.050091 restraints weight = 44092.922| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 30636 Z= 0.238 Angle : 0.586 8.852 41688 Z= 0.286 Chirality : 0.037 0.184 4808 Planarity : 0.004 0.046 5264 Dihedral : 3.704 24.250 4264 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.41 % Allowed : 11.49 % Favored : 87.11 % 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: 2.37 (0.14), residues: 3880 helix: 2.63 (0.10), residues: 2492 sheet: -0.05 (0.33), residues: 272 loop : -0.48 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1124 HIS 0.004 0.001 HIS A 173 PHE 0.014 0.001 PHE D 910 TYR 0.010 0.001 TYR C 577 ARG 0.004 0.000 ARG D1138 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 1916) hydrogen bonds : angle 4.27264 ( 5568) SS BOND : bond 0.00248 ( 4) SS BOND : angle 0.82671 ( 8) covalent geometry : bond 0.00526 (30632) covalent geometry : angle 0.58572 (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 186 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 3.149 Fit side-chains REVERT: A 284 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.6910 (mmt) REVERT: A 622 MET cc_start: 0.8522 (ttm) cc_final: 0.8051 (ttm) REVERT: A 625 ASP cc_start: 0.9080 (m-30) cc_final: 0.8805 (m-30) REVERT: A 637 ARG cc_start: 0.8178 (tmt170) cc_final: 0.7841 (ttp80) REVERT: B 284 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.6955 (mmt) REVERT: B 622 MET cc_start: 0.8519 (ttm) cc_final: 0.8069 (ttm) REVERT: B 625 ASP cc_start: 0.9075 (m-30) cc_final: 0.8793 (m-30) REVERT: B 637 ARG cc_start: 0.8166 (tmt170) cc_final: 0.7823 (ttp80) REVERT: C 284 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.6959 (mmt) REVERT: C 622 MET cc_start: 0.8543 (ttm) cc_final: 0.8144 (ttm) REVERT: C 625 ASP cc_start: 0.9077 (m-30) cc_final: 0.8793 (m-30) REVERT: C 637 ARG cc_start: 0.8153 (tmt170) cc_final: 0.7808 (ttp80) REVERT: D 284 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.6921 (mmt) REVERT: D 599 MET cc_start: 0.8639 (ttp) cc_final: 0.8437 (ttm) REVERT: D 622 MET cc_start: 0.8532 (ttm) cc_final: 0.8087 (ttm) REVERT: D 625 ASP cc_start: 0.9075 (m-30) cc_final: 0.8801 (m-30) REVERT: D 637 ARG cc_start: 0.8191 (tmt170) cc_final: 0.7840 (ttp80) outliers start: 41 outliers final: 22 residues processed: 173 average time/residue: 0.3908 time to fit residues: 113.4595 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 : 3.489 ------------------------------------------------------------------------------- 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 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 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 792 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: 0.8980 chunk 101 optimal weight: 7.9990 chunk 271 optimal weight: 0.7980 chunk 303 optimal weight: 30.0000 chunk 380 optimal weight: 10.0000 chunk 294 optimal weight: 10.0000 chunk 385 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 0.0970 chunk 99 optimal weight: 10.0000 chunk 199 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** ** B1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** D1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.067408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.049402 restraints weight = 146820.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.050996 restraints weight = 67349.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.052110 restraints weight = 41426.705| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30636 Z= 0.099 Angle : 0.466 7.065 41688 Z= 0.236 Chirality : 0.034 0.121 4808 Planarity : 0.004 0.046 5264 Dihedral : 3.604 21.566 4264 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.51 % Allowed : 12.65 % Favored : 86.83 % 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: 2.49 (0.14), residues: 3880 helix: 2.74 (0.10), residues: 2496 sheet: -0.47 (0.34), residues: 276 loop : -0.37 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 772 HIS 0.004 0.001 HIS A1002 PHE 0.015 0.001 PHE C 627 TYR 0.006 0.001 TYR C 211 ARG 0.003 0.000 ARG D1138 Details of bonding type rmsd hydrogen bonds : bond 0.03205 ( 1916) hydrogen bonds : angle 4.00639 ( 5568) SS BOND : bond 0.00355 ( 4) SS BOND : angle 0.73821 ( 8) covalent geometry : bond 0.00212 (30632) covalent geometry : angle 0.46589 (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 177 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 4.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 MET cc_start: 0.7346 (OUTLIER) cc_final: 0.6962 (mmt) REVERT: A 576 MET cc_start: 0.9247 (tpp) cc_final: 0.8925 (tpp) REVERT: A 599 MET cc_start: 0.8675 (ttm) cc_final: 0.8454 (ttm) REVERT: A 622 MET cc_start: 0.8473 (ttm) cc_final: 0.8049 (ttm) REVERT: A 625 ASP cc_start: 0.9085 (m-30) cc_final: 0.8806 (m-30) REVERT: A 927 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.8102 (mmm) REVERT: B 284 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.6935 (mmt) REVERT: B 576 MET cc_start: 0.9277 (tpp) cc_final: 0.8951 (tpp) REVERT: B 599 MET cc_start: 0.8682 (ttm) cc_final: 0.8452 (ttm) REVERT: B 622 MET cc_start: 0.8489 (ttm) cc_final: 0.8067 (ttm) REVERT: B 625 ASP cc_start: 0.9081 (m-30) cc_final: 0.8806 (m-30) REVERT: C 284 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.6992 (mmt) REVERT: C 576 MET cc_start: 0.9266 (tpp) cc_final: 0.9019 (tpp) REVERT: C 599 MET cc_start: 0.8667 (ttm) cc_final: 0.8455 (ttm) REVERT: C 622 MET cc_start: 0.8467 (ttm) cc_final: 0.8128 (ttm) REVERT: C 625 ASP cc_start: 0.9078 (m-30) cc_final: 0.8783 (m-30) REVERT: D 284 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.7008 (mmt) REVERT: D 576 MET cc_start: 0.9245 (tpp) cc_final: 0.8924 (tpp) REVERT: D 599 MET cc_start: 0.8630 (ttp) cc_final: 0.8263 (ttm) REVERT: D 622 MET cc_start: 0.8467 (ttm) cc_final: 0.8030 (ttm) REVERT: D 625 ASP cc_start: 0.9082 (m-30) cc_final: 0.8801 (m-30) outliers start: 15 outliers final: 4 residues processed: 162 average time/residue: 0.4741 time to fit residues: 130.8055 Evaluate side-chains 158 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 3.323 ------------------------------------------------------------------------------- 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 927 MET Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 614 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 134 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 394 optimal weight: 3.9990 chunk 245 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 232 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 357 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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** ** C1037 ASN ** 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 = 0.3470 r_free = 0.3470 target = 0.065729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.047849 restraints weight = 150953.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.049338 restraints weight = 70751.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.050385 restraints weight = 44183.479| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 30636 Z= 0.224 Angle : 0.566 6.666 41688 Z= 0.277 Chirality : 0.036 0.119 4808 Planarity : 0.004 0.048 5264 Dihedral : 3.651 23.309 4264 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.06 % Allowed : 12.76 % Favored : 86.18 % 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: 2.49 (0.14), residues: 3880 helix: 2.72 (0.11), residues: 2500 sheet: -0.72 (0.32), residues: 276 loop : -0.25 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1124 HIS 0.004 0.001 HIS C1002 PHE 0.013 0.001 PHE C 627 TYR 0.009 0.001 TYR A 577 ARG 0.003 0.000 ARG D 459 Details of bonding type rmsd hydrogen bonds : bond 0.03413 ( 1916) hydrogen bonds : angle 4.16484 ( 5568) SS BOND : bond 0.00237 ( 4) SS BOND : angle 0.79406 ( 8) covalent geometry : bond 0.00502 (30632) covalent geometry : angle 0.56637 (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 167 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 3.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.6985 (mmt) REVERT: A 576 MET cc_start: 0.9245 (tpp) cc_final: 0.8905 (tpp) REVERT: A 599 MET cc_start: 0.8707 (ttm) cc_final: 0.8452 (ttm) REVERT: A 622 MET cc_start: 0.8551 (ttm) cc_final: 0.8065 (ttm) REVERT: A 625 ASP cc_start: 0.9052 (m-30) cc_final: 0.8751 (m-30) REVERT: A 988 MET cc_start: 0.7772 (mtp) cc_final: 0.7256 (mtp) REVERT: B 284 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6965 (mmt) REVERT: B 581 MET cc_start: 0.8966 (mmp) cc_final: 0.8678 (mmp) REVERT: B 599 MET cc_start: 0.8720 (ttm) cc_final: 0.8498 (ttm) REVERT: B 622 MET cc_start: 0.8547 (ttm) cc_final: 0.8085 (ttm) REVERT: B 625 ASP cc_start: 0.9050 (m-30) cc_final: 0.8752 (m-30) REVERT: B 927 MET cc_start: 0.8375 (mmt) cc_final: 0.8073 (mmp) REVERT: B 988 MET cc_start: 0.7770 (mtp) cc_final: 0.7236 (mtp) REVERT: C 284 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6981 (mmt) REVERT: C 576 MET cc_start: 0.9204 (tpp) cc_final: 0.8922 (tpp) REVERT: C 581 MET cc_start: 0.8969 (mmp) cc_final: 0.8674 (mmp) REVERT: C 599 MET cc_start: 0.8703 (ttm) cc_final: 0.8482 (ttm) REVERT: C 622 MET cc_start: 0.8582 (ttm) cc_final: 0.8176 (ttm) REVERT: C 625 ASP cc_start: 0.9045 (m-30) cc_final: 0.8752 (m-30) REVERT: C 988 MET cc_start: 0.7792 (mtp) cc_final: 0.7256 (mtp) REVERT: D 284 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.6973 (mmt) REVERT: D 576 MET cc_start: 0.9245 (tpp) cc_final: 0.8880 (tpp) REVERT: D 599 MET cc_start: 0.8720 (ttp) cc_final: 0.8372 (ttp) REVERT: D 622 MET cc_start: 0.8558 (ttm) cc_final: 0.8052 (ttm) REVERT: D 625 ASP cc_start: 0.9067 (m-30) cc_final: 0.8783 (m-30) REVERT: D 637 ARG cc_start: 0.8197 (tmt170) cc_final: 0.7842 (ttp80) REVERT: D 988 MET cc_start: 0.7770 (mtp) cc_final: 0.7238 (mtp) outliers start: 31 outliers final: 21 residues processed: 157 average time/residue: 0.4266 time to fit residues: 114.6410 Evaluate side-chains 161 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 3.324 ------------------------------------------------------------------------------- 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 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 707 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain D residue 20 CYS Chi-restraints excluded: chain D residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 368 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 291 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 342 optimal weight: 0.3980 chunk 289 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 266 optimal weight: 0.1980 chunk 232 optimal weight: 20.0000 chunk 286 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3494 r_free = 0.3494 target = 0.066959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.048990 restraints weight = 147528.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.050537 restraints weight = 67859.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.051619 restraints weight = 42019.384| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 30636 Z= 0.108 Angle : 0.469 6.765 41688 Z= 0.235 Chirality : 0.034 0.118 4808 Planarity : 0.004 0.048 5264 Dihedral : 3.559 21.462 4264 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.86 % Allowed : 13.31 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.14), residues: 3880 helix: 2.83 (0.10), residues: 2500 sheet: -0.67 (0.32), residues: 276 loop : -0.27 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 772 HIS 0.002 0.000 HIS D 424 PHE 0.014 0.001 PHE C 627 TYR 0.005 0.001 TYR B1063 ARG 0.002 0.000 ARG D1138 Details of bonding type rmsd hydrogen bonds : bond 0.03111 ( 1916) hydrogen bonds : angle 3.95551 ( 5568) SS BOND : bond 0.00314 ( 4) SS BOND : angle 0.73127 ( 8) covalent geometry : bond 0.00243 (30632) covalent geometry : angle 0.46926 (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 170 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 3.187 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: 0.7349 (OUTLIER) cc_final: 0.6926 (mmt) REVERT: A 576 MET cc_start: 0.9233 (tpp) cc_final: 0.8925 (tpp) REVERT: A 599 MET cc_start: 0.8707 (ttm) cc_final: 0.8451 (ttm) REVERT: A 622 MET cc_start: 0.8486 (ttm) cc_final: 0.8109 (ttm) REVERT: A 625 ASP cc_start: 0.9014 (m-30) cc_final: 0.8728 (m-30) REVERT: B 284 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.6940 (mmt) REVERT: B 576 MET cc_start: 0.9257 (tpp) cc_final: 0.8937 (tpp) REVERT: B 599 MET cc_start: 0.8767 (ttm) cc_final: 0.8500 (ttm) REVERT: B 622 MET cc_start: 0.8479 (ttm) cc_final: 0.8091 (ttm) REVERT: B 625 ASP cc_start: 0.9007 (m-30) cc_final: 0.8711 (m-30) REVERT: C 284 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.6974 (mmt) REVERT: C 576 MET cc_start: 0.9238 (tpp) cc_final: 0.8986 (tpp) REVERT: C 599 MET cc_start: 0.8767 (ttm) cc_final: 0.8505 (ttm) REVERT: C 622 MET cc_start: 0.8484 (ttm) cc_final: 0.8132 (ttm) REVERT: C 625 ASP cc_start: 0.9002 (m-30) cc_final: 0.8709 (m-30) REVERT: D 284 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6936 (mmt) REVERT: D 576 MET cc_start: 0.9251 (tpp) cc_final: 0.8897 (tpp) REVERT: D 599 MET cc_start: 0.8747 (ttp) cc_final: 0.8521 (ttm) REVERT: D 622 MET cc_start: 0.8487 (ttm) cc_final: 0.8069 (ttm) REVERT: D 625 ASP cc_start: 0.9021 (m-30) cc_final: 0.8735 (m-30) outliers start: 25 outliers final: 20 residues processed: 161 average time/residue: 0.4050 time to fit residues: 113.3951 Evaluate side-chains 167 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 3.358 ------------------------------------------------------------------------------- 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 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 707 LEU 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 Chi-restraints excluded: chain D residue 983 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 78 optimal weight: 1.9990 chunk 133 optimal weight: 9.9990 chunk 254 optimal weight: 7.9990 chunk 231 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 297 optimal weight: 10.0000 chunk 295 optimal weight: 1.9990 chunk 104 optimal weight: 20.0000 chunk 307 optimal weight: 30.0000 chunk 92 optimal weight: 9.9990 chunk 287 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3476 r_free = 0.3476 target = 0.065900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.048113 restraints weight = 150774.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.049600 restraints weight = 70496.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.050616 restraints weight = 43592.707| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 30636 Z= 0.198 Angle : 0.544 7.007 41688 Z= 0.267 Chirality : 0.035 0.117 4808 Planarity : 0.004 0.048 5264 Dihedral : 3.564 22.870 4264 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.58 % Favored : 96.31 % Rotamer: Outliers : 0.93 % Allowed : 13.27 % Favored : 85.80 % 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: 2.58 (0.14), residues: 3880 helix: 2.81 (0.11), residues: 2500 sheet: -0.83 (0.31), residues: 276 loop : -0.23 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D1124 HIS 0.005 0.001 HIS C 505 PHE 0.013 0.001 PHE C 627 TYR 0.008 0.001 TYR A 577 ARG 0.002 0.000 ARG C 140 Details of bonding type rmsd hydrogen bonds : bond 0.03295 ( 1916) hydrogen bonds : angle 4.09246 ( 5568) SS BOND : bond 0.00266 ( 4) SS BOND : angle 0.75077 ( 8) covalent geometry : bond 0.00444 (30632) covalent geometry : angle 0.54426 (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 167 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 3.447 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: 0.7370 (OUTLIER) cc_final: 0.6979 (mmt) REVERT: A 576 MET cc_start: 0.9244 (tpp) cc_final: 0.8888 (tpp) REVERT: A 599 MET cc_start: 0.8752 (ttm) cc_final: 0.8481 (ttm) REVERT: A 622 MET cc_start: 0.8545 (ttm) cc_final: 0.8061 (ttm) REVERT: A 625 ASP cc_start: 0.9033 (m-30) cc_final: 0.8731 (m-30) REVERT: B 284 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.7001 (mmt) REVERT: B 576 MET cc_start: 0.9253 (tpp) cc_final: 0.8874 (tpp) REVERT: B 599 MET cc_start: 0.8790 (ttm) cc_final: 0.8523 (ttm) REVERT: B 622 MET cc_start: 0.8549 (ttm) cc_final: 0.8042 (ttm) REVERT: B 625 ASP cc_start: 0.9027 (m-30) cc_final: 0.8721 (m-30) REVERT: C 284 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.6993 (mmt) REVERT: C 576 MET cc_start: 0.9239 (tpp) cc_final: 0.8928 (tpp) REVERT: C 599 MET cc_start: 0.8775 (ttm) cc_final: 0.8511 (ttm) REVERT: C 622 MET cc_start: 0.8560 (ttm) cc_final: 0.8137 (ttm) REVERT: C 625 ASP cc_start: 0.9027 (m-30) cc_final: 0.8727 (m-30) REVERT: C 988 MET cc_start: 0.7685 (mtp) cc_final: 0.6808 (mtp) REVERT: D 284 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6985 (mmt) REVERT: D 576 MET cc_start: 0.9243 (tpp) cc_final: 0.8877 (tpp) REVERT: D 599 MET cc_start: 0.8814 (ttp) cc_final: 0.8454 (ttp) REVERT: D 622 MET cc_start: 0.8539 (ttm) cc_final: 0.8060 (ttm) REVERT: D 625 ASP cc_start: 0.9028 (m-30) cc_final: 0.8724 (m-30) outliers start: 27 outliers final: 22 residues processed: 156 average time/residue: 0.3797 time to fit residues: 101.7005 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 : 3.397 ------------------------------------------------------------------------------- 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 B residue 20 CYS Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 983 MET Chi-restraints excluded: chain 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 218 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 293 optimal weight: 6.9990 chunk 319 optimal weight: 7.9990 chunk 300 optimal weight: 30.0000 chunk 364 optimal weight: 2.9990 chunk 284 optimal weight: 0.7980 chunk 35 optimal weight: 9.9990 chunk 123 optimal weight: 0.9980 chunk 186 optimal weight: 3.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.066149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.048348 restraints weight = 149925.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.049867 restraints weight = 70117.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.050948 restraints weight = 43756.621| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30636 Z= 0.162 Angle : 0.516 8.132 41688 Z= 0.255 Chirality : 0.035 0.159 4808 Planarity : 0.004 0.046 5264 Dihedral : 3.584 22.510 4264 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.09 % Favored : 96.80 % Rotamer: Outliers : 0.93 % Allowed : 13.72 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.81 (0.10), residues: 2512 sheet: -0.87 (0.31), residues: 276 loop : -0.30 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1124 HIS 0.003 0.001 HIS B 505 PHE 0.016 0.001 PHE D 910 TYR 0.006 0.001 TYR B1063 ARG 0.004 0.000 ARG C 508 Details of bonding type rmsd hydrogen bonds : bond 0.03226 ( 1916) hydrogen bonds : angle 4.05019 ( 5568) SS BOND : bond 0.00267 ( 4) SS BOND : angle 0.71899 ( 8) covalent geometry : bond 0.00366 (30632) covalent geometry : angle 0.51566 (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 170 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 3.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.6990 (mmt) REVERT: A 576 MET cc_start: 0.9226 (tpp) cc_final: 0.8868 (tpp) REVERT: A 622 MET cc_start: 0.8558 (ttm) cc_final: 0.8104 (ttm) REVERT: A 625 ASP cc_start: 0.9052 (m-30) cc_final: 0.8743 (m-30) REVERT: B 284 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.7004 (mmt) REVERT: B 576 MET cc_start: 0.9263 (tpp) cc_final: 0.8889 (tpp) REVERT: B 599 MET cc_start: 0.8803 (ttm) cc_final: 0.8531 (ttm) REVERT: B 622 MET cc_start: 0.8549 (ttm) cc_final: 0.8093 (ttm) REVERT: B 625 ASP cc_start: 0.9040 (m-30) cc_final: 0.8731 (m-30) REVERT: C 284 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.7051 (mmt) REVERT: C 576 MET cc_start: 0.9245 (tpp) cc_final: 0.8931 (tpp) REVERT: C 599 MET cc_start: 0.8791 (ttm) cc_final: 0.8521 (ttm) REVERT: C 622 MET cc_start: 0.8554 (ttm) cc_final: 0.8131 (ttm) REVERT: C 625 ASP cc_start: 0.9042 (m-30) cc_final: 0.8737 (m-30) REVERT: C 988 MET cc_start: 0.7658 (mtp) cc_final: 0.6735 (mtp) REVERT: D 284 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.6989 (mmt) REVERT: D 576 MET cc_start: 0.9263 (tpp) cc_final: 0.8892 (tpp) REVERT: D 599 MET cc_start: 0.8841 (ttp) cc_final: 0.8529 (ttp) REVERT: D 622 MET cc_start: 0.8560 (ttm) cc_final: 0.8078 (ttm) REVERT: D 625 ASP cc_start: 0.9040 (m-30) cc_final: 0.8731 (m-30) outliers start: 27 outliers final: 23 residues processed: 159 average time/residue: 0.3802 time to fit residues: 103.0408 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 : 3.510 ------------------------------------------------------------------------------- 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 1034 LEU Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 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 707 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain D residue 20 CYS Chi-restraints excluded: chain D residue 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 1034 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 343 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 338 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 311 optimal weight: 20.0000 chunk 375 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 340 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.3480 r_free = 0.3480 target = 0.066045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.048514 restraints weight = 150110.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.050029 restraints weight = 69465.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.051078 restraints weight = 43055.931| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30636 Z= 0.125 Angle : 0.502 8.620 41688 Z= 0.249 Chirality : 0.035 0.154 4808 Planarity : 0.004 0.048 5264 Dihedral : 3.522 21.827 4264 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.04 % Favored : 96.86 % Rotamer: Outliers : 0.99 % Allowed : 13.58 % Favored : 85.43 % 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: 2520 sheet: -0.85 (0.31), residues: 276 loop : -0.28 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 772 HIS 0.003 0.001 HIS D 505 PHE 0.013 0.001 PHE C 627 TYR 0.006 0.001 TYR B1063 ARG 0.003 0.000 ARG D 508 Details of bonding type rmsd hydrogen bonds : bond 0.03143 ( 1916) hydrogen bonds : angle 3.99323 ( 5568) SS BOND : bond 0.00299 ( 4) SS BOND : angle 0.69585 ( 8) covalent geometry : bond 0.00284 (30632) covalent geometry : angle 0.50244 (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 170 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 6.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.7020 (mmt) REVERT: A 576 MET cc_start: 0.9237 (tpp) cc_final: 0.8914 (tpp) REVERT: A 622 MET cc_start: 0.8550 (ttm) cc_final: 0.8106 (ttm) REVERT: A 625 ASP cc_start: 0.9064 (m-30) cc_final: 0.8749 (m-30) REVERT: B 284 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.7015 (mmt) REVERT: B 576 MET cc_start: 0.9278 (tpp) cc_final: 0.8940 (tpp) REVERT: B 599 MET cc_start: 0.8786 (ttm) cc_final: 0.8497 (ttm) REVERT: B 622 MET cc_start: 0.8544 (ttm) cc_final: 0.8098 (ttm) REVERT: B 625 ASP cc_start: 0.9056 (m-30) cc_final: 0.8743 (m-30) REVERT: C 284 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.7055 (mmt) REVERT: C 576 MET cc_start: 0.9260 (tpp) cc_final: 0.8982 (tpp) REVERT: C 599 MET cc_start: 0.8776 (ttm) cc_final: 0.8506 (ttm) REVERT: C 622 MET cc_start: 0.8558 (ttm) cc_final: 0.8157 (ttm) REVERT: C 625 ASP cc_start: 0.9060 (m-30) cc_final: 0.8747 (m-30) REVERT: C 988 MET cc_start: 0.7605 (mtp) cc_final: 0.7112 (mtp) REVERT: D 284 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.7016 (mmt) REVERT: D 576 MET cc_start: 0.9277 (tpp) cc_final: 0.8910 (tpp) REVERT: D 622 MET cc_start: 0.8551 (ttm) cc_final: 0.8107 (ttm) REVERT: D 625 ASP cc_start: 0.9056 (m-30) cc_final: 0.8739 (m-30) outliers start: 29 outliers final: 24 residues processed: 158 average time/residue: 0.5306 time to fit residues: 150.3587 Evaluate side-chains 167 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 9.656 ------------------------------------------------------------------------------- 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 1034 LEU Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 284 MET Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain D residue 20 CYS Chi-restraints excluded: chain D residue 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 1034 LEU 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: 10.0000 chunk 104 optimal weight: 20.0000 chunk 85 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 278 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 260 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.066309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.048722 restraints weight = 150614.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.050214 restraints weight = 69397.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.051262 restraints weight = 43020.628| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30636 Z= 0.120 Angle : 0.494 8.203 41688 Z= 0.246 Chirality : 0.035 0.147 4808 Planarity : 0.004 0.048 5264 Dihedral : 3.495 21.399 4264 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.73 % Favored : 97.16 % Rotamer: Outliers : 0.99 % Allowed : 13.82 % Favored : 85.19 % 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: 2.55 (0.14), residues: 3880 helix: 2.79 (0.10), residues: 2520 sheet: -0.96 (0.31), residues: 280 loop : -0.26 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 772 HIS 0.005 0.000 HIS D 505 PHE 0.013 0.001 PHE D 910 TYR 0.005 0.001 TYR B1063 ARG 0.008 0.000 ARG D 601 Details of bonding type rmsd hydrogen bonds : bond 0.03090 ( 1916) hydrogen bonds : angle 3.97148 ( 5568) SS BOND : bond 0.00317 ( 4) SS BOND : angle 0.69301 ( 8) covalent geometry : bond 0.00273 (30632) covalent geometry : angle 0.49400 (41680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10971.00 seconds wall clock time: 196 minutes 54.62 seconds (11814.62 seconds total)