Starting phenix.real_space_refine on Sat Aug 10 19:22:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b93_44367/08_2024/9b93_44367.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b93_44367/08_2024/9b93_44367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b93_44367/08_2024/9b93_44367.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b93_44367/08_2024/9b93_44367.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b93_44367/08_2024/9b93_44367.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b93_44367/08_2024/9b93_44367.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 152 5.16 5 C 19328 2.51 5 N 5272 2.21 5 O 5056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 625": "OD1" <-> "OD2" Residue "A PHE 899": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1055": "OD1" <-> "OD2" Residue "B PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 625": "OD1" <-> "OD2" Residue "B PHE 899": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1055": "OD1" <-> "OD2" Residue "C PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 625": "OD1" <-> "OD2" Residue "C PHE 899": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1055": "OD1" <-> "OD2" Residue "D PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 625": "OD1" <-> "OD2" Residue "D PHE 899": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1055": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 29808 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 7452 Classifications: {'peptide': 984} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PTRANS': 43, 'TRANS': 940} Chain breaks: 10 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 385 Unresolved non-hydrogen angles: 476 Unresolved non-hydrogen dihedrals: 312 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 18, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 269 Chain: "B" Number of atoms: 7452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 7452 Classifications: {'peptide': 984} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PTRANS': 43, 'TRANS': 940} Chain breaks: 10 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 385 Unresolved non-hydrogen angles: 476 Unresolved non-hydrogen dihedrals: 312 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 18, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 269 Chain: "C" Number of atoms: 7452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 7452 Classifications: {'peptide': 984} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PTRANS': 43, 'TRANS': 940} Chain breaks: 10 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 385 Unresolved non-hydrogen angles: 476 Unresolved non-hydrogen dihedrals: 312 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 18, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 269 Chain: "D" Number of atoms: 7452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 7452 Classifications: {'peptide': 984} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PTRANS': 43, 'TRANS': 940} Chain breaks: 10 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 385 Unresolved non-hydrogen angles: 476 Unresolved non-hydrogen dihedrals: 312 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 18, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 269 Time building chain proxies: 15.91, per 1000 atoms: 0.53 Number of scatterers: 29808 At special positions: 0 Unit cell: (164.772, 163.944, 162.288, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 152 16.00 O 5056 8.00 N 5272 7.00 C 19328 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 37 " distance=2.94 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 37 " distance=2.03 Simple disulfide: pdb=" SG CYS A 993 " - pdb=" SG CYS A1011 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 37 " distance=2.94 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 37 " distance=2.03 Simple disulfide: pdb=" SG CYS B 993 " - pdb=" SG CYS B1011 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 37 " distance=2.94 Simple disulfide: pdb=" SG CYS C 35 " - pdb=" SG CYS C 37 " distance=2.03 Simple disulfide: pdb=" SG CYS C 993 " - pdb=" SG CYS C1011 " distance=2.03 Simple disulfide: pdb=" SG CYS D 20 " - pdb=" SG CYS D 37 " distance=2.94 Simple disulfide: pdb=" SG CYS D 35 " - pdb=" SG CYS D 37 " distance=2.03 Simple disulfide: pdb=" SG CYS D 993 " - pdb=" SG CYS D1011 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 11.48 Conformation dependent library (CDL) restraints added in 5.4 seconds 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7304 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 16 sheets defined 69.0% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 98 through 108 removed outlier: 3.792A pdb=" N VAL A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 141 Processing helix chain 'A' and resid 141 through 150 Processing helix chain 'A' and resid 160 through 178 removed outlier: 3.757A pdb=" N HIS A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR A 178 " --> pdb=" O GLN A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 201 removed outlier: 4.186A pdb=" N LEU A 200 " --> pdb=" O ASN A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 258 Processing helix chain 'A' and resid 264 through 268 removed outlier: 3.840A pdb=" N THR A 267 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY A 268 " --> pdb=" O GLY A 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 264 through 268' Processing helix chain 'A' and resid 281 through 294 removed outlier: 3.618A pdb=" N THR A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 318 removed outlier: 3.507A pdb=" N THR A 318 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 337 removed outlier: 3.729A pdb=" N GLY A 329 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 removed outlier: 4.425A pdb=" N GLN A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 372 through 386 removed outlier: 3.801A pdb=" N ILE A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.690A pdb=" N ALA A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 435 Processing helix chain 'A' and resid 437 through 447 Processing helix chain 'A' and resid 450 through 455 Processing helix chain 'A' and resid 456 through 465 Processing helix chain 'A' and resid 471 through 480 Processing helix chain 'A' and resid 502 through 512 removed outlier: 3.781A pdb=" N VAL A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 569 Processing helix chain 'A' and resid 571 through 582 Processing helix chain 'A' and resid 585 through 602 removed outlier: 3.581A pdb=" N LEU A 602 " --> pdb=" O VAL A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 634 removed outlier: 3.582A pdb=" N SER A 633 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 644 Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 669 through 681 Processing helix chain 'A' and resid 689 through 699 Processing helix chain 'A' and resid 700 through 705 Processing helix chain 'A' and resid 767 through 778 Processing helix chain 'A' and resid 778 through 803 Processing helix chain 'A' and resid 811 through 834 Processing helix chain 'A' and resid 852 through 862 removed outlier: 3.643A pdb=" N ASP A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 884 Processing helix chain 'A' and resid 887 through 910 removed outlier: 3.595A pdb=" N MET A 900 " --> pdb=" O CYS A 896 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU A 906 " --> pdb=" O PHE A 902 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU A 907 " --> pdb=" O THR A 903 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N HIS A 908 " --> pdb=" O VAL A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 926 removed outlier: 3.725A pdb=" N SER A 924 " --> pdb=" O ILE A 920 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 925 " --> pdb=" O VAL A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 953 Processing helix chain 'A' and resid 958 through 967 Processing helix chain 'A' and resid 967 through 975 removed outlier: 3.808A pdb=" N ILE A 974 " --> pdb=" O PRO A 970 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE A 975 " --> pdb=" O TYR A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 984 removed outlier: 3.597A pdb=" N MET A 983 " --> pdb=" O PRO A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1033 Processing helix chain 'A' and resid 1033 through 1072 removed outlier: 4.953A pdb=" N GLY A1052 " --> pdb=" O GLY A1048 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ASN A1053 " --> pdb=" O LYS A1049 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ARG A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1078 No H-bonds generated for 'chain 'A' and resid 1076 through 1078' Processing helix chain 'A' and resid 1079 through 1088 removed outlier: 4.194A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1143 Processing helix chain 'A' and resid 1143 through 1177 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 98 through 108 removed outlier: 3.791A pdb=" N VAL B 102 " --> pdb=" O ASP B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 141 Processing helix chain 'B' and resid 141 through 150 Processing helix chain 'B' and resid 160 through 178 removed outlier: 3.757A pdb=" N HIS B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR B 178 " --> pdb=" O GLN B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 201 removed outlier: 4.186A pdb=" N LEU B 200 " --> pdb=" O ASN B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 258 Processing helix chain 'B' and resid 264 through 268 removed outlier: 3.841A pdb=" N THR B 267 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY B 268 " --> pdb=" O GLY B 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 264 through 268' Processing helix chain 'B' and resid 281 through 294 removed outlier: 3.617A pdb=" N THR B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 318 removed outlier: 3.507A pdb=" N THR B 318 " --> pdb=" O THR B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 337 removed outlier: 3.729A pdb=" N GLY B 329 " --> pdb=" O GLY B 325 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 356 removed outlier: 4.423A pdb=" N GLN B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 359 No H-bonds generated for 'chain 'B' and resid 357 through 359' Processing helix chain 'B' and resid 372 through 386 removed outlier: 3.800A pdb=" N ILE B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 405 through 415 removed outlier: 3.690A pdb=" N ALA B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 435 Processing helix chain 'B' and resid 437 through 447 Processing helix chain 'B' and resid 450 through 455 Processing helix chain 'B' and resid 456 through 465 Processing helix chain 'B' and resid 471 through 480 Processing helix chain 'B' and resid 502 through 512 removed outlier: 3.780A pdb=" N VAL B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 569 Processing helix chain 'B' and resid 571 through 582 Processing helix chain 'B' and resid 585 through 602 removed outlier: 3.581A pdb=" N LEU B 602 " --> pdb=" O VAL B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 634 removed outlier: 3.582A pdb=" N SER B 633 " --> pdb=" O GLU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 644 Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 663 through 668 Processing helix chain 'B' and resid 669 through 681 Processing helix chain 'B' and resid 689 through 699 Processing helix chain 'B' and resid 700 through 705 Processing helix chain 'B' and resid 767 through 778 Processing helix chain 'B' and resid 778 through 803 Processing helix chain 'B' and resid 811 through 834 Processing helix chain 'B' and resid 852 through 862 removed outlier: 3.643A pdb=" N ASP B 862 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 884 Processing helix chain 'B' and resid 887 through 910 removed outlier: 3.596A pdb=" N MET B 900 " --> pdb=" O CYS B 896 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU B 906 " --> pdb=" O PHE B 902 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU B 907 " --> pdb=" O THR B 903 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N HIS B 908 " --> pdb=" O VAL B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 926 removed outlier: 3.726A pdb=" N SER B 924 " --> pdb=" O ILE B 920 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS B 925 " --> pdb=" O VAL B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 953 Processing helix chain 'B' and resid 958 through 967 Processing helix chain 'B' and resid 967 through 975 removed outlier: 3.808A pdb=" N ILE B 974 " --> pdb=" O PRO B 970 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE B 975 " --> pdb=" O TYR B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 984 removed outlier: 3.598A pdb=" N MET B 983 " --> pdb=" O PRO B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1033 Processing helix chain 'B' and resid 1033 through 1072 removed outlier: 4.953A pdb=" N GLY B1052 " --> pdb=" O GLY B1048 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ASN B1053 " --> pdb=" O LYS B1049 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR B1063 " --> pdb=" O LYS B1059 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ARG B1064 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1078 No H-bonds generated for 'chain 'B' and resid 1076 through 1078' Processing helix chain 'B' and resid 1079 through 1088 removed outlier: 4.193A pdb=" N SER B1083 " --> pdb=" O PHE B1079 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1143 Processing helix chain 'B' and resid 1143 through 1177 Processing helix chain 'C' and resid 10 through 15 Processing helix chain 'C' and resid 98 through 108 removed outlier: 3.791A pdb=" N VAL C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 141 Processing helix chain 'C' and resid 141 through 150 Processing helix chain 'C' and resid 160 through 178 removed outlier: 3.758A pdb=" N HIS C 165 " --> pdb=" O GLY C 161 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR C 178 " --> pdb=" O GLN C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 201 removed outlier: 4.187A pdb=" N LEU C 200 " --> pdb=" O ASN C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 258 Processing helix chain 'C' and resid 264 through 268 removed outlier: 3.841A pdb=" N THR C 267 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY C 268 " --> pdb=" O GLY C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 268' Processing helix chain 'C' and resid 281 through 294 removed outlier: 3.618A pdb=" N THR C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 318 removed outlier: 3.506A pdb=" N THR C 318 " --> pdb=" O THR C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 337 removed outlier: 3.729A pdb=" N GLY C 329 " --> pdb=" O GLY C 325 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 356 removed outlier: 4.424A pdb=" N GLN C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 359 No H-bonds generated for 'chain 'C' and resid 357 through 359' Processing helix chain 'C' and resid 372 through 386 removed outlier: 3.801A pdb=" N ILE C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 405 through 415 removed outlier: 3.690A pdb=" N ALA C 409 " --> pdb=" O ARG C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 435 Processing helix chain 'C' and resid 437 through 447 Processing helix chain 'C' and resid 450 through 455 Processing helix chain 'C' and resid 456 through 465 Processing helix chain 'C' and resid 471 through 480 Processing helix chain 'C' and resid 502 through 512 removed outlier: 3.780A pdb=" N VAL C 506 " --> pdb=" O ASP C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 569 Processing helix chain 'C' and resid 571 through 582 Processing helix chain 'C' and resid 585 through 602 removed outlier: 3.581A pdb=" N LEU C 602 " --> pdb=" O VAL C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 634 removed outlier: 3.582A pdb=" N SER C 633 " --> pdb=" O GLU C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 644 Processing helix chain 'C' and resid 653 through 661 Processing helix chain 'C' and resid 663 through 668 Processing helix chain 'C' and resid 669 through 681 Processing helix chain 'C' and resid 689 through 699 Processing helix chain 'C' and resid 700 through 705 Processing helix chain 'C' and resid 767 through 778 Processing helix chain 'C' and resid 778 through 803 Processing helix chain 'C' and resid 811 through 834 Processing helix chain 'C' and resid 852 through 862 removed outlier: 3.644A pdb=" N ASP C 862 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 884 Processing helix chain 'C' and resid 887 through 910 removed outlier: 3.595A pdb=" N MET C 900 " --> pdb=" O CYS C 896 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU C 906 " --> pdb=" O PHE C 902 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU C 907 " --> pdb=" O THR C 903 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N HIS C 908 " --> pdb=" O VAL C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 926 removed outlier: 3.725A pdb=" N SER C 924 " --> pdb=" O ILE C 920 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS C 925 " --> pdb=" O VAL C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 953 Processing helix chain 'C' and resid 958 through 967 Processing helix chain 'C' and resid 967 through 975 removed outlier: 3.807A pdb=" N ILE C 974 " --> pdb=" O PRO C 970 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE C 975 " --> pdb=" O TYR C 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 984 removed outlier: 3.597A pdb=" N MET C 983 " --> pdb=" O PRO C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1033 removed outlier: 3.500A pdb=" N VAL C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1072 removed outlier: 4.954A pdb=" N GLY C1052 " --> pdb=" O GLY C1048 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASN C1053 " --> pdb=" O LYS C1049 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR C1063 " --> pdb=" O LYS C1059 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ARG C1064 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1078 No H-bonds generated for 'chain 'C' and resid 1076 through 1078' Processing helix chain 'C' and resid 1079 through 1088 removed outlier: 4.194A pdb=" N SER C1083 " --> pdb=" O PHE C1079 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1143 Processing helix chain 'C' and resid 1143 through 1177 Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 98 through 108 removed outlier: 3.792A pdb=" N VAL D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 141 Processing helix chain 'D' and resid 141 through 150 Processing helix chain 'D' and resid 160 through 178 removed outlier: 3.757A pdb=" N HIS D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR D 178 " --> pdb=" O GLN D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 201 removed outlier: 4.186A pdb=" N LEU D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 258 Processing helix chain 'D' and resid 264 through 268 removed outlier: 3.840A pdb=" N THR D 267 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY D 268 " --> pdb=" O GLY D 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 264 through 268' Processing helix chain 'D' and resid 281 through 294 removed outlier: 3.618A pdb=" N THR D 286 " --> pdb=" O GLU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 318 removed outlier: 3.507A pdb=" N THR D 318 " --> pdb=" O THR D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 337 removed outlier: 3.729A pdb=" N GLY D 329 " --> pdb=" O GLY D 325 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 356 removed outlier: 4.425A pdb=" N GLN D 348 " --> pdb=" O LEU D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 359 No H-bonds generated for 'chain 'D' and resid 357 through 359' Processing helix chain 'D' and resid 372 through 386 removed outlier: 3.801A pdb=" N ILE D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 403 Processing helix chain 'D' and resid 405 through 415 removed outlier: 3.691A pdb=" N ALA D 409 " --> pdb=" O ARG D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 435 Processing helix chain 'D' and resid 437 through 447 Processing helix chain 'D' and resid 450 through 455 Processing helix chain 'D' and resid 456 through 465 Processing helix chain 'D' and resid 471 through 480 Processing helix chain 'D' and resid 502 through 512 removed outlier: 3.780A pdb=" N VAL D 506 " --> pdb=" O ASP D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 569 Processing helix chain 'D' and resid 571 through 582 Processing helix chain 'D' and resid 585 through 602 removed outlier: 3.581A pdb=" N LEU D 602 " --> pdb=" O VAL D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 634 removed outlier: 3.581A pdb=" N SER D 633 " --> pdb=" O GLU D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 644 Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 663 through 668 Processing helix chain 'D' and resid 669 through 681 Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 700 through 705 Processing helix chain 'D' and resid 767 through 778 Processing helix chain 'D' and resid 778 through 803 Processing helix chain 'D' and resid 811 through 834 Processing helix chain 'D' and resid 852 through 862 removed outlier: 3.642A pdb=" N ASP D 862 " --> pdb=" O LEU D 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 884 Processing helix chain 'D' and resid 887 through 910 removed outlier: 3.597A pdb=" N MET D 900 " --> pdb=" O CYS D 896 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU D 906 " --> pdb=" O PHE D 902 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU D 907 " --> pdb=" O THR D 903 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N HIS D 908 " --> pdb=" O VAL D 904 " (cutoff:3.500A) Processing helix chain 'D' and resid 916 through 926 removed outlier: 3.725A pdb=" N SER D 924 " --> pdb=" O ILE D 920 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS D 925 " --> pdb=" O VAL D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 953 Processing helix chain 'D' and resid 958 through 967 Processing helix chain 'D' and resid 967 through 975 removed outlier: 3.808A pdb=" N ILE D 974 " --> pdb=" O PRO D 970 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE D 975 " --> pdb=" O TYR D 971 " (cutoff:3.500A) Processing helix chain 'D' and resid 979 through 984 removed outlier: 3.597A pdb=" N MET D 983 " --> pdb=" O PRO D 979 " (cutoff:3.500A) Processing helix chain 'D' and resid 1016 through 1033 removed outlier: 3.500A pdb=" N VAL D1020 " --> pdb=" O ALA D1016 " (cutoff:3.500A) Processing helix chain 'D' and resid 1033 through 1072 removed outlier: 4.954A pdb=" N GLY D1052 " --> pdb=" O GLY D1048 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ASN D1053 " --> pdb=" O LYS D1049 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR D1063 " --> pdb=" O LYS D1059 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ARG D1064 " --> pdb=" O ALA D1060 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1078 No H-bonds generated for 'chain 'D' and resid 1076 through 1078' Processing helix chain 'D' and resid 1079 through 1088 removed outlier: 4.194A pdb=" N SER D1083 " --> pdb=" O PHE D1079 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1143 Processing helix chain 'D' and resid 1143 through 1177 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 94 removed outlier: 6.492A pdb=" N LEU A 93 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ALA A 185 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N PHE A 233 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLY A 187 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL A 235 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA A 189 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ILE A 153 " --> pdb=" O MET A 186 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL A 188 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR A 155 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LEU A 299 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU A 275 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N VAL A 301 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU A 277 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N CYS A 298 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N TYR A 364 " --> pdb=" O CYS A 298 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU A 300 " --> pdb=" O TYR A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 989 through 990 removed outlier: 4.162A pdb=" N GLU A 989 " --> pdb=" O HIS A1002 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 19 Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 78 Processing sheet with id=AA7, first strand: chain 'B' and resid 92 through 94 removed outlier: 6.493A pdb=" N LEU B 93 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA B 185 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N PHE B 233 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLY B 187 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL B 235 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA B 189 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ILE B 153 " --> pdb=" O MET B 186 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL B 188 " --> pdb=" O ILE B 153 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR B 155 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LEU B 299 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU B 275 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL B 301 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU B 277 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N CYS B 298 " --> pdb=" O THR B 362 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N TYR B 364 " --> pdb=" O CYS B 298 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU B 300 " --> pdb=" O TYR B 364 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 989 through 990 removed outlier: 4.162A pdb=" N GLU B 989 " --> pdb=" O HIS B1002 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 16 through 19 Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 78 Processing sheet with id=AB2, first strand: chain 'C' and resid 92 through 94 removed outlier: 6.491A pdb=" N LEU C 93 " --> pdb=" O ASP C 236 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA C 185 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N PHE C 233 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLY C 187 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL C 235 " --> pdb=" O GLY C 187 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA C 189 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ILE C 153 " --> pdb=" O MET C 186 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL C 188 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR C 155 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LEU C 299 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU C 275 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL C 301 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU C 277 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N CYS C 298 " --> pdb=" O THR C 362 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N TYR C 364 " --> pdb=" O CYS C 298 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU C 300 " --> pdb=" O TYR C 364 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 989 through 990 removed outlier: 4.161A pdb=" N GLU C 989 " --> pdb=" O HIS C1002 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 16 through 19 Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 78 Processing sheet with id=AB6, first strand: chain 'D' and resid 92 through 94 removed outlier: 6.491A pdb=" N LEU D 93 " --> pdb=" O ASP D 236 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA D 185 " --> pdb=" O ALA D 231 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N PHE D 233 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLY D 187 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL D 235 " --> pdb=" O GLY D 187 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA D 189 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ILE D 153 " --> pdb=" O MET D 186 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL D 188 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N THR D 155 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N LEU D 299 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU D 275 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL D 301 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU D 277 " --> pdb=" O VAL D 301 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N CYS D 298 " --> pdb=" O THR D 362 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TYR D 364 " --> pdb=" O CYS D 298 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU D 300 " --> pdb=" O TYR D 364 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 989 through 990 removed outlier: 4.162A pdb=" N GLU D 989 " --> pdb=" O HIS D1002 " (cutoff:3.500A) 1890 hydrogen bonds defined for protein. 5586 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.30 Time building geometry restraints manager: 12.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9672 1.35 - 1.47: 7356 1.47 - 1.59: 13228 1.59 - 1.71: 0 1.71 - 1.83: 232 Bond restraints: 30488 Sorted by residual: bond pdb=" N SER C 469 " pdb=" CA SER C 469 " ideal model delta sigma weight residual 1.457 1.474 -0.016 1.29e-02 6.01e+03 1.58e+00 bond pdb=" N SER A 469 " pdb=" CA SER A 469 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.55e+00 bond pdb=" N SER D 469 " pdb=" CA SER D 469 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.51e+00 bond pdb=" N SER B 469 " pdb=" CA SER B 469 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.45e+00 bond pdb=" N PRO D 809 " pdb=" CA PRO D 809 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.31e-02 5.83e+03 1.15e+00 ... (remaining 30483 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.89: 936 106.89 - 113.69: 16935 113.69 - 120.49: 11681 120.49 - 127.29: 11506 127.29 - 134.09: 418 Bond angle restraints: 41476 Sorted by residual: angle pdb=" C SER A 469 " pdb=" CA SER A 469 " pdb=" CB SER A 469 " ideal model delta sigma weight residual 110.42 115.48 -5.06 1.99e+00 2.53e-01 6.46e+00 angle pdb=" C SER B 469 " pdb=" CA SER B 469 " pdb=" CB SER B 469 " ideal model delta sigma weight residual 110.42 115.46 -5.04 1.99e+00 2.53e-01 6.42e+00 angle pdb=" C SER C 469 " pdb=" CA SER C 469 " pdb=" CB SER C 469 " ideal model delta sigma weight residual 110.42 115.45 -5.03 1.99e+00 2.53e-01 6.38e+00 angle pdb=" C GLY C 263 " pdb=" N VAL C 264 " pdb=" CA VAL C 264 " ideal model delta sigma weight residual 121.97 126.47 -4.50 1.80e+00 3.09e-01 6.26e+00 angle pdb=" C SER D 469 " pdb=" CA SER D 469 " pdb=" CB SER D 469 " ideal model delta sigma weight residual 110.42 115.39 -4.97 1.99e+00 2.53e-01 6.24e+00 ... (remaining 41471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 15407 16.52 - 33.03: 1900 33.03 - 49.55: 481 49.55 - 66.06: 108 66.06 - 82.58: 28 Dihedral angle restraints: 17924 sinusoidal: 6640 harmonic: 11284 Sorted by residual: dihedral pdb=" CB CYS B 993 " pdb=" SG CYS B 993 " pdb=" SG CYS B1011 " pdb=" CB CYS B1011 " ideal model delta sinusoidal sigma weight residual 93.00 145.15 -52.15 1 1.00e+01 1.00e-02 3.71e+01 dihedral pdb=" CB CYS D 993 " pdb=" SG CYS D 993 " pdb=" SG CYS D1011 " pdb=" CB CYS D1011 " ideal model delta sinusoidal sigma weight residual 93.00 145.10 -52.10 1 1.00e+01 1.00e-02 3.70e+01 dihedral pdb=" CB CYS C 993 " pdb=" SG CYS C 993 " pdb=" SG CYS C1011 " pdb=" CB CYS C1011 " ideal model delta sinusoidal sigma weight residual 93.00 145.08 -52.08 1 1.00e+01 1.00e-02 3.70e+01 ... (remaining 17921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 3089 0.025 - 0.050: 1096 0.050 - 0.075: 402 0.075 - 0.100: 150 0.100 - 0.125: 55 Chirality restraints: 4792 Sorted by residual: chirality pdb=" CA ILE C 278 " pdb=" N ILE C 278 " pdb=" C ILE C 278 " pdb=" CB ILE C 278 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CA ILE B 278 " pdb=" N ILE B 278 " pdb=" C ILE B 278 " pdb=" CB ILE B 278 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.89e-01 chirality pdb=" CA ILE D 24 " pdb=" N ILE D 24 " pdb=" C ILE D 24 " pdb=" CB ILE D 24 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.84e-01 ... (remaining 4789 not shown) Planarity restraints: 5228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A1076 " 0.028 5.00e-02 4.00e+02 4.25e-02 2.90e+00 pdb=" N PRO A1077 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A1077 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1077 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B1076 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.87e+00 pdb=" N PRO B1077 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B1077 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B1077 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D1076 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO D1077 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO D1077 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D1077 " 0.023 5.00e-02 4.00e+02 ... (remaining 5225 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1645 2.74 - 3.28: 31266 3.28 - 3.82: 50866 3.82 - 4.36: 57142 4.36 - 4.90: 100695 Nonbonded interactions: 241614 Sorted by model distance: nonbonded pdb=" OG1 THR D 155 " pdb=" OH TYR D 229 " model vdw 2.197 3.040 nonbonded pdb=" OG1 THR B 155 " pdb=" OH TYR B 229 " model vdw 2.197 3.040 nonbonded pdb=" OG1 THR C 155 " pdb=" OH TYR C 229 " model vdw 2.198 3.040 nonbonded pdb=" OG1 THR A 155 " pdb=" OH TYR A 229 " model vdw 2.198 3.040 nonbonded pdb=" O SER C 63 " pdb=" OG1 THR C 67 " model vdw 2.200 3.040 ... (remaining 241609 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.150 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 77.730 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 30488 Z= 0.125 Angle : 0.461 6.337 41476 Z= 0.238 Chirality : 0.033 0.125 4792 Planarity : 0.004 0.043 5228 Dihedral : 15.662 82.581 10584 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.07 % Allowed : 22.14 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.13), residues: 3848 helix: 2.26 (0.10), residues: 2416 sheet: -0.64 (0.42), residues: 192 loop : -0.43 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1058 HIS 0.006 0.001 HIS C 505 PHE 0.006 0.001 PHE D 933 TYR 0.004 0.001 TYR D1015 ARG 0.003 0.000 ARG A1119 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 3.574 Fit side-chains REVERT: A 625 ASP cc_start: 0.8949 (m-30) cc_final: 0.8748 (m-30) REVERT: A 988 MET cc_start: 0.8947 (mtm) cc_final: 0.8616 (ptp) REVERT: B 186 MET cc_start: 0.9139 (mmm) cc_final: 0.8816 (mmm) REVERT: B 1034 LEU cc_start: 0.9307 (mp) cc_final: 0.8865 (tt) outliers start: 2 outliers final: 1 residues processed: 126 average time/residue: 0.3549 time to fit residues: 78.9581 Evaluate side-chains 121 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 3.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 936 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 9.9990 chunk 297 optimal weight: 20.0000 chunk 164 optimal weight: 7.9990 chunk 101 optimal weight: 20.0000 chunk 200 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 chunk 307 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 186 optimal weight: 8.9990 chunk 228 optimal weight: 20.0000 chunk 355 optimal weight: 0.5980 overall best weight: 6.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN A 424 HIS A 584 ASN A 656 GLN A 786 ASN A1014 GLN A1017 ASN B 228 ASN B 424 HIS B 584 ASN B 656 GLN B 786 ASN B1017 ASN C 228 ASN C 424 HIS C 584 ASN C 656 GLN C 786 ASN C1017 ASN D 228 ASN D 424 HIS D 584 ASN D 656 GLN D 786 ASN D1017 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 30488 Z= 0.539 Angle : 0.647 7.313 41476 Z= 0.336 Chirality : 0.041 0.152 4792 Planarity : 0.005 0.053 5228 Dihedral : 3.874 45.439 4242 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.03 % Allowed : 20.70 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.14), residues: 3848 helix: 2.58 (0.10), residues: 2516 sheet: -0.36 (0.37), residues: 236 loop : -0.52 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 680 HIS 0.006 0.001 HIS B 173 PHE 0.017 0.002 PHE D 627 TYR 0.013 0.001 TYR D1015 ARG 0.005 0.000 ARG C 327 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 123 time to evaluate : 3.514 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8858 (ttt-90) REVERT: A 1118 GLU cc_start: 0.9286 (OUTLIER) cc_final: 0.9051 (tm-30) REVERT: B 92 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8065 (ttt180) REVERT: B 926 MET cc_start: 0.9251 (mmt) cc_final: 0.8956 (mmt) REVERT: B 1017 ASN cc_start: 0.8767 (OUTLIER) cc_final: 0.8262 (t0) REVERT: B 1118 GLU cc_start: 0.9318 (OUTLIER) cc_final: 0.9055 (tm-30) REVERT: C 92 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8036 (ttt180) REVERT: C 509 MET cc_start: 0.8413 (mmp) cc_final: 0.8193 (mmp) REVERT: C 926 MET cc_start: 0.9268 (mmt) cc_final: 0.8935 (mmt) REVERT: C 1118 GLU cc_start: 0.9320 (OUTLIER) cc_final: 0.9012 (pp20) REVERT: D 1146 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8386 (mp0) outliers start: 88 outliers final: 41 residues processed: 192 average time/residue: 0.4328 time to fit residues: 136.3986 Evaluate side-chains 164 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 115 time to evaluate : 3.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 927 MET Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 1017 ASN Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1146 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1017 ASN Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1118 GLU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 787 VAL Chi-restraints excluded: chain C residue 833 LEU Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1017 ASN Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1118 GLU Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1146 GLU Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 787 VAL Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 1017 ASN Chi-restraints excluded: chain D residue 1146 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 20.0000 chunk 110 optimal weight: 0.9990 chunk 296 optimal weight: 20.0000 chunk 242 optimal weight: 0.7980 chunk 98 optimal weight: 10.0000 chunk 356 optimal weight: 0.7980 chunk 385 optimal weight: 6.9990 chunk 317 optimal weight: 8.9990 chunk 353 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 286 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 HIS A1017 ASN B1014 GLN B1017 ASN C1014 GLN D1014 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30488 Z= 0.212 Angle : 0.489 6.343 41476 Z= 0.256 Chirality : 0.036 0.126 4792 Planarity : 0.004 0.047 5228 Dihedral : 3.762 22.536 4240 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.51 % Allowed : 20.87 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3848 helix: 2.77 (0.10), residues: 2516 sheet: -0.51 (0.36), residues: 236 loop : -0.54 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1058 HIS 0.004 0.001 HIS C 424 PHE 0.014 0.001 PHE C 627 TYR 0.013 0.001 TYR D1015 ARG 0.005 0.000 ARG C 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 125 time to evaluate : 3.211 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.7805 (ttt180) REVERT: A 284 MET cc_start: 0.9207 (mmm) cc_final: 0.8912 (mmm) REVERT: A 1017 ASN cc_start: 0.8109 (OUTLIER) cc_final: 0.7811 (t0) REVERT: B 92 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8667 (ttt-90) REVERT: B 509 MET cc_start: 0.8304 (mmp) cc_final: 0.8098 (mmp) REVERT: B 926 MET cc_start: 0.9189 (mmt) cc_final: 0.8944 (mmt) REVERT: B 936 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.8610 (m-80) REVERT: B 1017 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.7749 (t0) REVERT: C 926 MET cc_start: 0.9181 (mmt) cc_final: 0.8939 (mmt) REVERT: D 92 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8277 (ttt-90) REVERT: D 284 MET cc_start: 0.9178 (mmm) cc_final: 0.8860 (mmm) REVERT: D 625 ASP cc_start: 0.9037 (m-30) cc_final: 0.8812 (m-30) REVERT: D 1118 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8901 (pp20) outliers start: 73 outliers final: 36 residues processed: 181 average time/residue: 0.3554 time to fit residues: 110.3278 Evaluate side-chains 163 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 120 time to evaluate : 3.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1017 ASN Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 1017 ASN Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 936 PHE Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1118 GLU Chi-restraints excluded: chain D residue 1165 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 8.9990 chunk 268 optimal weight: 0.9980 chunk 185 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 239 optimal weight: 3.9990 chunk 357 optimal weight: 7.9990 chunk 378 optimal weight: 4.9990 chunk 186 optimal weight: 0.9990 chunk 339 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1014 GLN C1017 ASN D1014 GLN D1017 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 30488 Z= 0.193 Angle : 0.467 7.704 41476 Z= 0.243 Chirality : 0.036 0.125 4792 Planarity : 0.004 0.046 5228 Dihedral : 3.678 22.298 4240 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.10 % Allowed : 20.35 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.14), residues: 3848 helix: 2.85 (0.10), residues: 2520 sheet: -0.58 (0.36), residues: 236 loop : -0.53 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1058 HIS 0.005 0.001 HIS B 424 PHE 0.014 0.001 PHE B 627 TYR 0.010 0.001 TYR C1015 ARG 0.006 0.000 ARG B1166 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 126 time to evaluate : 3.521 Fit side-chains REVERT: A 92 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8455 (ttt-90) REVERT: A 284 MET cc_start: 0.9147 (mmm) cc_final: 0.8929 (mmm) REVERT: A 625 ASP cc_start: 0.9031 (m-30) cc_final: 0.8764 (m-30) REVERT: A 1017 ASN cc_start: 0.8155 (OUTLIER) cc_final: 0.7934 (t0) REVERT: B 92 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8259 (ttt-90) REVERT: B 872 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8876 (mm) REVERT: B 1017 ASN cc_start: 0.8229 (OUTLIER) cc_final: 0.7802 (t0) REVERT: B 1037 ASN cc_start: 0.9507 (m-40) cc_final: 0.9283 (m-40) REVERT: B 1118 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.8984 (tm-30) REVERT: B 1156 ASP cc_start: 0.8982 (m-30) cc_final: 0.8614 (m-30) REVERT: C 92 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.7837 (ttt-90) REVERT: C 872 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8996 (mm) REVERT: C 1118 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.8947 (pp20) REVERT: C 1156 ASP cc_start: 0.9059 (m-30) cc_final: 0.8709 (m-30) REVERT: D 92 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8723 (ttt-90) REVERT: D 625 ASP cc_start: 0.9058 (m-30) cc_final: 0.8818 (m-30) REVERT: D 784 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8429 (ttm) REVERT: D 1118 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8897 (pp20) outliers start: 90 outliers final: 49 residues processed: 202 average time/residue: 0.3652 time to fit residues: 125.9252 Evaluate side-chains 181 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 120 time to evaluate : 3.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1017 ASN Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1146 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 927 MET Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1017 ASN Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1118 GLU Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1017 ASN Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1118 GLU Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1146 GLU Chi-restraints excluded: chain C residue 1165 ILE Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 936 PHE Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1118 GLU Chi-restraints excluded: chain D residue 1165 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 0.7980 chunk 215 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 282 optimal weight: 0.9980 chunk 156 optimal weight: 8.9990 chunk 323 optimal weight: 20.0000 chunk 261 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 193 optimal weight: 8.9990 chunk 340 optimal weight: 0.0370 chunk 95 optimal weight: 4.9990 overall best weight: 3.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1014 GLN ** D1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30488 Z= 0.284 Angle : 0.493 6.402 41476 Z= 0.255 Chirality : 0.036 0.124 4792 Planarity : 0.004 0.047 5228 Dihedral : 3.673 22.888 4240 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.17 % Allowed : 20.63 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.14), residues: 3848 helix: 2.87 (0.10), residues: 2520 sheet: -0.66 (0.36), residues: 236 loop : -0.57 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 680 HIS 0.004 0.001 HIS B 424 PHE 0.015 0.001 PHE B 627 TYR 0.012 0.001 TYR C1015 ARG 0.005 0.000 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 123 time to evaluate : 3.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8133 (ttt-90) REVERT: A 613 LYS cc_start: 0.9422 (OUTLIER) cc_final: 0.9220 (mttm) REVERT: A 625 ASP cc_start: 0.9051 (m-30) cc_final: 0.8797 (m-30) REVERT: A 784 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8424 (ttm) REVERT: B 872 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8890 (mm) REVERT: B 1037 ASN cc_start: 0.9494 (m-40) cc_final: 0.9254 (m-40) REVERT: B 1118 GLU cc_start: 0.9268 (OUTLIER) cc_final: 0.9003 (tm-30) REVERT: C 872 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.9003 (mm) REVERT: C 1118 GLU cc_start: 0.9249 (OUTLIER) cc_final: 0.8970 (pp20) REVERT: D 625 ASP cc_start: 0.9080 (m-30) cc_final: 0.8837 (m-30) REVERT: D 784 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8477 (ttm) REVERT: D 1118 GLU cc_start: 0.9191 (OUTLIER) cc_final: 0.8934 (pp20) outliers start: 92 outliers final: 58 residues processed: 196 average time/residue: 0.3636 time to fit residues: 122.3540 Evaluate side-chains 189 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 122 time to evaluate : 3.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 613 LYS Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1146 GLU Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1118 GLU Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 684 MET Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 787 VAL Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 983 MET Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1118 GLU Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1146 GLU Chi-restraints excluded: chain C residue 1165 ILE Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain D residue 787 VAL Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1118 GLU Chi-restraints excluded: chain D residue 1125 GLU Chi-restraints excluded: chain D residue 1165 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 40.0000 chunk 341 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 379 optimal weight: 1.9990 chunk 314 optimal weight: 1.9990 chunk 175 optimal weight: 0.7980 chunk 31 optimal weight: 20.0000 chunk 125 optimal weight: 20.0000 chunk 199 optimal weight: 40.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1017 ASN C1161 GLN D1014 GLN ** D1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 30488 Z= 0.182 Angle : 0.453 6.547 41476 Z= 0.235 Chirality : 0.035 0.126 4792 Planarity : 0.003 0.045 5228 Dihedral : 3.622 21.343 4240 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.69 % Allowed : 21.11 % Favored : 76.21 % 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: 2.66 (0.14), residues: 3848 helix: 2.91 (0.10), residues: 2528 sheet: -0.69 (0.36), residues: 236 loop : -0.51 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1058 HIS 0.006 0.001 HIS A 505 PHE 0.013 0.001 PHE D 423 TYR 0.008 0.001 TYR B1015 ARG 0.005 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 127 time to evaluate : 3.447 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8460 (ttt-90) REVERT: A 625 ASP cc_start: 0.9046 (m-30) cc_final: 0.8767 (m-30) REVERT: A 784 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8343 (ttm) REVERT: C 1118 GLU cc_start: 0.9213 (OUTLIER) cc_final: 0.8942 (pp20) REVERT: C 1156 ASP cc_start: 0.9087 (m-30) cc_final: 0.8708 (m-30) REVERT: D 625 ASP cc_start: 0.9069 (m-30) cc_final: 0.8788 (m-30) REVERT: D 784 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8416 (ttm) REVERT: D 1118 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.8922 (pp20) REVERT: D 1130 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8674 (mm-30) outliers start: 78 outliers final: 51 residues processed: 192 average time/residue: 0.3562 time to fit residues: 118.7337 Evaluate side-chains 177 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 121 time to evaluate : 3.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1146 GLU Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1118 GLU Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1017 ASN Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain C residue 1118 GLU Chi-restraints excluded: chain C residue 1146 GLU Chi-restraints excluded: chain C residue 1165 ILE Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1014 GLN Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1118 GLU Chi-restraints excluded: chain D residue 1165 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 216 optimal weight: 0.9980 chunk 276 optimal weight: 0.7980 chunk 214 optimal weight: 6.9990 chunk 319 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 377 optimal weight: 0.0050 chunk 236 optimal weight: 4.9990 chunk 230 optimal weight: 7.9990 chunk 174 optimal weight: 8.9990 overall best weight: 2.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1017 ASN D1017 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 30488 Z= 0.250 Angle : 0.481 8.019 41476 Z= 0.247 Chirality : 0.036 0.142 4792 Planarity : 0.004 0.046 5228 Dihedral : 3.602 21.720 4240 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.72 % Allowed : 21.21 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.14), residues: 3848 helix: 2.93 (0.10), residues: 2528 sheet: -0.70 (0.36), residues: 236 loop : -0.52 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 680 HIS 0.003 0.001 HIS A 505 PHE 0.014 0.001 PHE A 627 TYR 0.016 0.001 TYR D1015 ARG 0.009 0.000 ARG D 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 119 time to evaluate : 3.733 Fit side-chains REVERT: A 92 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8448 (ttt-90) REVERT: A 625 ASP cc_start: 0.9061 (m-30) cc_final: 0.8782 (m-30) REVERT: A 784 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8307 (ttm) REVERT: B 1017 ASN cc_start: 0.8514 (OUTLIER) cc_final: 0.8084 (t0) REVERT: B 1118 GLU cc_start: 0.9240 (OUTLIER) cc_final: 0.8976 (tm-30) REVERT: C 1118 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.8957 (pp20) REVERT: D 625 ASP cc_start: 0.9076 (m-30) cc_final: 0.8670 (m-30) REVERT: D 784 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8454 (ttm) REVERT: D 1118 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.8941 (pp20) REVERT: D 1130 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8687 (mm-30) outliers start: 79 outliers final: 56 residues processed: 186 average time/residue: 0.3325 time to fit residues: 109.3939 Evaluate side-chains 182 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 119 time to evaluate : 3.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1146 GLU Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1017 ASN Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1118 GLU Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 787 VAL Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 983 MET Chi-restraints excluded: chain C residue 1014 GLN Chi-restraints excluded: chain C residue 1017 ASN Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1118 GLU Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1165 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1014 GLN Chi-restraints excluded: chain D residue 1017 ASN Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1118 GLU Chi-restraints excluded: chain D residue 1165 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 225 optimal weight: 40.0000 chunk 113 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 240 optimal weight: 6.9990 chunk 257 optimal weight: 6.9990 chunk 186 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 296 optimal weight: 20.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1161 GLN ** B1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1014 GLN ** D1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 30488 Z= 0.419 Angle : 0.566 7.348 41476 Z= 0.288 Chirality : 0.039 0.189 4792 Planarity : 0.004 0.049 5228 Dihedral : 3.711 23.254 4240 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.96 % Allowed : 21.04 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.57 (0.14), residues: 3848 helix: 2.86 (0.10), residues: 2520 sheet: -0.70 (0.36), residues: 236 loop : -0.59 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 680 HIS 0.005 0.001 HIS A1128 PHE 0.018 0.001 PHE D 627 TYR 0.013 0.001 TYR B1015 ARG 0.008 0.000 ARG D 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 117 time to evaluate : 3.738 Fit side-chains revert: symmetry clash REVERT: A 625 ASP cc_start: 0.9070 (m-30) cc_final: 0.8838 (m-30) REVERT: A 784 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8388 (ttm) REVERT: A 1017 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8494 (t0) REVERT: B 1017 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8398 (t0) REVERT: B 1118 GLU cc_start: 0.9301 (OUTLIER) cc_final: 0.9044 (tm-30) REVERT: C 1118 GLU cc_start: 0.9282 (OUTLIER) cc_final: 0.8998 (pp20) REVERT: D 625 ASP cc_start: 0.9102 (m-30) cc_final: 0.8836 (m-30) REVERT: D 784 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8500 (ttm) REVERT: D 1118 GLU cc_start: 0.9255 (OUTLIER) cc_final: 0.9005 (pp20) REVERT: D 1130 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8680 (mm-30) outliers start: 86 outliers final: 55 residues processed: 188 average time/residue: 0.3258 time to fit residues: 108.9761 Evaluate side-chains 179 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 117 time to evaluate : 3.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 787 VAL Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1017 ASN Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1146 GLU Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1017 ASN Chi-restraints excluded: chain B residue 1089 LEU Chi-restraints excluded: chain B residue 1118 GLU Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 653 THR Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 787 VAL Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 983 MET Chi-restraints excluded: chain C residue 1014 GLN Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1118 GLU Chi-restraints excluded: chain C residue 1125 GLU Chi-restraints excluded: chain C residue 1165 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 784 MET Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1014 GLN Chi-restraints excluded: chain D residue 1118 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 0.9980 chunk 361 optimal weight: 1.9990 chunk 330 optimal weight: 4.9990 chunk 352 optimal weight: 2.9990 chunk 211 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 276 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 318 optimal weight: 1.9990 chunk 332 optimal weight: 0.6980 chunk 350 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1017 ASN ** C1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1014 GLN ** D1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 30488 Z= 0.155 Angle : 0.467 10.233 41476 Z= 0.239 Chirality : 0.035 0.243 4792 Planarity : 0.003 0.046 5228 Dihedral : 3.656 20.381 4240 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.79 % Allowed : 22.25 % Favored : 75.96 % 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: 2.70 (0.14), residues: 3848 helix: 2.94 (0.10), residues: 2528 sheet: -0.74 (0.36), residues: 236 loop : -0.50 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1058 HIS 0.003 0.001 HIS C 424 PHE 0.014 0.001 PHE D 423 TYR 0.007 0.001 TYR B1015 ARG 0.006 0.000 ARG D 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 121 time to evaluate : 3.360 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8463 (ttt-90) REVERT: A 625 ASP cc_start: 0.9047 (m-30) cc_final: 0.8768 (m-30) REVERT: A 784 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8294 (ttm) REVERT: B 1017 ASN cc_start: 0.8355 (OUTLIER) cc_final: 0.7937 (t0) REVERT: C 1118 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.8943 (pp20) REVERT: D 625 ASP cc_start: 0.9062 (m-30) cc_final: 0.8655 (m-30) REVERT: D 1118 GLU cc_start: 0.9180 (OUTLIER) cc_final: 0.8927 (pp20) outliers start: 52 outliers final: 43 residues processed: 166 average time/residue: 0.3526 time to fit residues: 102.8158 Evaluate side-chains 165 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 117 time to evaluate : 4.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1146 GLU Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1017 ASN Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1118 GLU Chi-restraints excluded: chain B residue 1165 ILE Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1014 GLN Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1118 GLU Chi-restraints excluded: chain C residue 1165 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1118 GLU Chi-restraints excluded: chain D residue 1165 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 0.0980 chunk 372 optimal weight: 4.9990 chunk 227 optimal weight: 9.9990 chunk 176 optimal weight: 4.9990 chunk 258 optimal weight: 0.8980 chunk 390 optimal weight: 4.9990 chunk 359 optimal weight: 0.9990 chunk 310 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 240 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30488 Z= 0.214 Angle : 0.486 10.519 41476 Z= 0.247 Chirality : 0.036 0.249 4792 Planarity : 0.003 0.046 5228 Dihedral : 3.599 20.807 4240 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.86 % Allowed : 22.21 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.14), residues: 3848 helix: 3.00 (0.10), residues: 2512 sheet: -0.72 (0.36), residues: 236 loop : -0.46 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 579 HIS 0.011 0.001 HIS A 505 PHE 0.014 0.001 PHE D 423 TYR 0.009 0.001 TYR D1015 ARG 0.007 0.000 ARG D 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7696 Ramachandran restraints generated. 3848 Oldfield, 0 Emsley, 3848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 119 time to evaluate : 3.427 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8444 (ttt-90) REVERT: A 625 ASP cc_start: 0.9054 (m-30) cc_final: 0.8752 (m-30) REVERT: A 784 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8306 (ttm) REVERT: A 988 MET cc_start: 0.9008 (mtm) cc_final: 0.8704 (ptp) REVERT: C 1118 GLU cc_start: 0.9231 (OUTLIER) cc_final: 0.8957 (pp20) REVERT: D 625 ASP cc_start: 0.9063 (m-30) cc_final: 0.8670 (m-30) REVERT: D 1118 GLU cc_start: 0.9198 (OUTLIER) cc_final: 0.8950 (pp20) outliers start: 54 outliers final: 46 residues processed: 166 average time/residue: 0.3424 time to fit residues: 100.0061 Evaluate side-chains 169 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 119 time to evaluate : 3.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 653 THR Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 784 MET Chi-restraints excluded: chain A residue 798 SER Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 936 PHE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1146 GLU Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 653 THR Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 867 CYS Chi-restraints excluded: chain B residue 936 PHE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1118 GLU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 936 PHE Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1014 GLN Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1088 LEU Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1118 GLU Chi-restraints excluded: chain C residue 1165 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 653 THR Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain D residue 867 CYS Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 983 MET Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1118 GLU Chi-restraints excluded: chain D residue 1165 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 6.9990 chunk 331 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 286 optimal weight: 0.0570 chunk 45 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 311 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 319 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS ** B1014 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1017 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.066468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.049069 restraints weight = 111245.567| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.45 r_work: 0.2690 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 30488 Z= 0.195 Angle : 0.475 11.536 41476 Z= 0.241 Chirality : 0.036 0.239 4792 Planarity : 0.003 0.046 5228 Dihedral : 3.571 19.839 4240 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.89 % Allowed : 22.14 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.14), residues: 3848 helix: 3.02 (0.10), residues: 2512 sheet: -0.71 (0.36), residues: 236 loop : -0.45 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 579 HIS 0.012 0.001 HIS B 505 PHE 0.014 0.001 PHE D 423 TYR 0.008 0.001 TYR D1015 ARG 0.006 0.000 ARG D 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5177.50 seconds wall clock time: 94 minutes 2.59 seconds (5642.59 seconds total)