Starting phenix.real_space_refine on Mon Aug 25 05:45:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fu8_29455/08_2025/8fu8_29455_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fu8_29455/08_2025/8fu8_29455.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fu8_29455/08_2025/8fu8_29455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fu8_29455/08_2025/8fu8_29455.map" model { file = "/net/cci-nas-00/data/ceres_data/8fu8_29455/08_2025/8fu8_29455_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fu8_29455/08_2025/8fu8_29455_neut.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 109 5.16 5 C 16192 2.51 5 N 4177 2.21 5 O 4991 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 159 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25469 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1046, 8183 Classifications: {'peptide': 1046} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 989} Chain breaks: 4 Chain: "B" Number of atoms: 8360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1069, 8360 Classifications: {'peptide': 1069} Link IDs: {'PTRANS': 55, 'TRANS': 1013} Chain breaks: 2 Chain: "C" Number of atoms: 8211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1050, 8211 Classifications: {'peptide': 1050} Link IDs: {'PTRANS': 53, 'TRANS': 996} Chain breaks: 5 Chain: "A" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 253 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 224 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 238 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.87, per 1000 atoms: 0.23 Number of scatterers: 25469 At special positions: 0 Unit cell: (137.313, 155.621, 163.111, 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 109 16.00 O 4991 8.00 N 4177 7.00 C 16192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1206 " - " ASN A 225 " " NAG A1215 " - " ASN A1082 " " NAG B1210 " - " ASN B 61 " " NAG C1204 " - " ASN C 225 " " NAG C1212 " - " ASN C 315 " Time building additional restraints: 2.21 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5920 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 42 sheets defined 23.8% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 278 through 288 Processing helix chain 'A' and resid 322 through 327 Processing helix chain 'A' and resid 333 through 337 removed outlier: 3.529A pdb=" N TRP A 337 " --> pdb=" O VAL A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 370 through 373 Processing helix chain 'A' and resid 390 through 395 Processing helix chain 'A' and resid 400 through 406 Processing helix chain 'A' and resid 607 through 612 Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 730 through 738 Processing helix chain 'A' and resid 739 through 741 No H-bonds generated for 'chain 'A' and resid 739 through 741' Processing helix chain 'A' and resid 742 through 767 removed outlier: 3.532A pdb=" N ASP A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 810 Processing helix chain 'A' and resid 850 through 869 Processing helix chain 'A' and resid 870 through 874 Processing helix chain 'A' and resid 881 through 892 Processing helix chain 'A' and resid 896 through 902 removed outlier: 4.132A pdb=" N LEU A 900 " --> pdb=" O THR A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 925 Processing helix chain 'A' and resid 929 through 949 removed outlier: 3.946A pdb=" N VAL A 935 " --> pdb=" O LYS A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 952 No H-bonds generated for 'chain 'A' and resid 950 through 952' Processing helix chain 'A' and resid 960 through 966 Processing helix chain 'A' and resid 969 through 1017 removed outlier: 4.295A pdb=" N VAL A 975 " --> pdb=" O PRO A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1130 Processing helix chain 'B' and resid 277 through 287 removed outlier: 4.051A pdb=" N SER B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 327 Processing helix chain 'B' and resid 333 through 337 removed outlier: 3.931A pdb=" N TRP B 337 " --> pdb=" O VAL B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 354 Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.292A pdb=" N ASN B 372 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 603 through 608 Processing helix chain 'B' and resid 609 through 613 Processing helix chain 'B' and resid 614 through 619 removed outlier: 3.655A pdb=" N VAL B 619 " --> pdb=" O PRO B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 727 Processing helix chain 'B' and resid 730 through 737 Processing helix chain 'B' and resid 738 through 741 Processing helix chain 'B' and resid 742 through 767 removed outlier: 3.751A pdb=" N ASP B 759 " --> pdb=" O ALA B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 810 Processing helix chain 'B' and resid 850 through 869 Processing helix chain 'B' and resid 870 through 874 Processing helix chain 'B' and resid 881 through 891 Processing helix chain 'B' and resid 896 through 902 removed outlier: 4.185A pdb=" N LEU B 900 " --> pdb=" O THR B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 923 removed outlier: 3.802A pdb=" N ILE B 918 " --> pdb=" O ALA B 914 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN B 919 " --> pdb=" O ILE B 915 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP B 920 " --> pdb=" O GLY B 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 949 removed outlier: 3.894A pdb=" N VAL B 935 " --> pdb=" O LYS B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 952 No H-bonds generated for 'chain 'B' and resid 950 through 952' Processing helix chain 'B' and resid 961 through 966 Processing helix chain 'B' and resid 969 through 1017 removed outlier: 3.897A pdb=" N VAL B 975 " --> pdb=" O PRO B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 1125 through 1130 removed outlier: 3.670A pdb=" N LEU B1129 " --> pdb=" O LEU B1125 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 288 Processing helix chain 'C' and resid 348 through 354 removed outlier: 4.097A pdb=" N LEU C 352 " --> pdb=" O ASP C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 373 Processing helix chain 'C' and resid 721 through 727 Processing helix chain 'C' and resid 730 through 738 removed outlier: 4.227A pdb=" N LEU C 736 " --> pdb=" O GLU C 732 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 738 " --> pdb=" O SER C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 741 No H-bonds generated for 'chain 'C' and resid 739 through 741' Processing helix chain 'C' and resid 742 through 767 removed outlier: 3.809A pdb=" N ASP C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 800 through 810 Processing helix chain 'C' and resid 850 through 868 Processing helix chain 'C' and resid 870 through 874 Processing helix chain 'C' and resid 881 through 892 Processing helix chain 'C' and resid 896 through 902 removed outlier: 4.277A pdb=" N LEU C 900 " --> pdb=" O THR C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 923 Processing helix chain 'C' and resid 925 through 928 Processing helix chain 'C' and resid 929 through 949 removed outlier: 3.949A pdb=" N VAL C 935 " --> pdb=" O LYS C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 950 through 952 No H-bonds generated for 'chain 'C' and resid 950 through 952' Processing helix chain 'C' and resid 960 through 968 Processing helix chain 'C' and resid 970 through 1017 removed outlier: 3.876A pdb=" N VAL C 975 " --> pdb=" O PRO C 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 1125 through 1130 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 30 removed outlier: 7.883A pdb=" N ASN A 61 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N TYR A 253 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER A 196 " --> pdb=" O PRO A 216 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 36 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.757A pdb=" N ASP A 271 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 295 through 300 removed outlier: 6.951A pdb=" N VAL A 579 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 312 removed outlier: 4.782A pdb=" N GLU A 308 " --> pdb=" O CYS A 522 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ASP A 558 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE A 549 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 338 through 342 removed outlier: 3.642A pdb=" N VAL A 379 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N CYS A 345 " --> pdb=" O CYS A 509 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 338 through 342 removed outlier: 3.642A pdb=" N VAL A 379 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ASN A 378 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU A 500 " --> pdb=" O ASN A 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 436 through 437 removed outlier: 4.589A pdb=" N LEU A 436 " --> pdb=" O LEU A 476 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 638 through 639 removed outlier: 6.587A pdb=" N ILE A 654 " --> pdb=" O ILE A 650 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 685 through 688 removed outlier: 6.571A pdb=" N ALA A 685 " --> pdb=" O ILE B 772 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LYS B 774 " --> pdb=" O ALA A 685 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ASN A 687 " --> pdb=" O LYS B 774 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 695 through 698 removed outlier: 3.740A pdb=" N ALA A1062 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE A1079 " --> pdb=" O ALA A1062 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 712 removed outlier: 5.866A pdb=" N TYR A1051 " --> pdb=" O HIS A1032 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N HIS A1032 " --> pdb=" O TYR A1051 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 720 removed outlier: 4.164A pdb=" N LYS A 717 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 771 through 774 Processing sheet with id=AB7, first strand: chain 'A' and resid 1104 through 1109 removed outlier: 4.904A pdb=" N ALA A1071 " --> pdb=" O SER A1107 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 29 through 31 removed outlier: 7.874A pdb=" N ASN B 61 " --> pdb=" O TYR B 253 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N TYR B 253 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER B 196 " --> pdb=" O PRO B 216 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.515A pdb=" N THR B 258 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ASP B 274 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU B 260 " --> pdb=" O ALA B 272 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA B 272 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LYS B 262 " --> pdb=" O THR B 270 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.509A pdb=" N PHE B 159 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 295 through 303 removed outlier: 5.379A pdb=" N ILE B 296 " --> pdb=" O THR B 583 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR B 583 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N GLN B 298 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL B 581 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER B 300 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY B 578 " --> pdb=" O GLN B 597 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 309 through 312 removed outlier: 5.227A pdb=" N ASP B 558 " --> pdb=" O ILE B 571 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA B 559 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE B 549 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 338 through 342 removed outlier: 6.586A pdb=" N CYS B 345 " --> pdb=" O CYS B 509 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 338 through 342 removed outlier: 5.432A pdb=" N ASN B 378 " --> pdb=" O GLU B 500 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLU B 500 " --> pdb=" O ASN B 378 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 638 through 639 removed outlier: 6.604A pdb=" N ILE B 654 " --> pdb=" O ILE B 650 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 686 through 688 Processing sheet with id=AC8, first strand: chain 'B' and resid 695 through 712 removed outlier: 6.560A pdb=" N SER B 695 " --> pdb=" O THR B1060 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N THR B1060 " --> pdb=" O SER B 695 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA B 697 " --> pdb=" O ASN B1058 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASN B1058 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N GLU B1056 " --> pdb=" O PRO B 699 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N TYR B1051 " --> pdb=" O HIS B1032 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N HIS B1032 " --> pdb=" O TYR B1051 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 695 through 712 removed outlier: 6.560A pdb=" N SER B 695 " --> pdb=" O THR B1060 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N THR B1060 " --> pdb=" O SER B 695 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA B 697 " --> pdb=" O ASN B1058 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASN B1058 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N GLU B1056 " --> pdb=" O PRO B 699 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA B1062 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N PHE B1079 " --> pdb=" O ALA B1062 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLN B1090 " --> pdb=" O GLU B1095 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLU B1095 " --> pdb=" O GLN B1090 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 717 through 720 removed outlier: 4.269A pdb=" N LYS B 717 " --> pdb=" O LEU B 845 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1104 through 1109 removed outlier: 4.785A pdb=" N ALA B1071 " --> pdb=" O SER B1107 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.546A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N ASN C 61 " --> pdb=" O TYR C 253 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N TYR C 253 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N PHE C 192 " --> pdb=" O ASP C 219 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASP C 219 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE C 194 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.367A pdb=" N THR C 258 " --> pdb=" O ASP C 274 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ASP C 274 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU C 260 " --> pdb=" O ALA C 272 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ALA C 272 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LYS C 262 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 159 through 163 removed outlier: 3.890A pdb=" N GLY C 103 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 178 through 180 Processing sheet with id=AD7, first strand: chain 'C' and resid 295 through 303 removed outlier: 5.209A pdb=" N ILE C 296 " --> pdb=" O THR C 583 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N THR C 583 " --> pdb=" O ILE C 296 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLN C 298 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL C 581 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY C 578 " --> pdb=" O GLN C 597 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 308 through 312 removed outlier: 3.961A pdb=" N GLU C 308 " --> pdb=" O CYS C 522 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 338 through 342 removed outlier: 3.901A pdb=" N VAL C 379 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N CYS C 345 " --> pdb=" O CYS C 509 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 338 through 342 removed outlier: 3.901A pdb=" N VAL C 379 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ASN C 378 " --> pdb=" O GLU C 500 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLU C 500 " --> pdb=" O ASN C 378 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR C 492 " --> pdb=" O ILE C 386 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 638 through 639 removed outlier: 6.576A pdb=" N ILE C 654 " --> pdb=" O ILE C 650 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 695 through 712 removed outlier: 7.045A pdb=" N GLN C1055 " --> pdb=" O THR C 700 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N PHE C 702 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ILE C 704 " --> pdb=" O TYR C1051 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N TYR C1051 " --> pdb=" O ILE C 704 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL C 706 " --> pdb=" O VAL C1049 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL C1049 " --> pdb=" O VAL C 706 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR C 708 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU C1047 " --> pdb=" O THR C 708 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE C 710 " --> pdb=" O VAL C1045 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL C1045 " --> pdb=" O ILE C 710 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLY C1043 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N TYR C1051 " --> pdb=" O HIS C1032 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N HIS C1032 " --> pdb=" O TYR C1051 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 695 through 712 removed outlier: 7.045A pdb=" N GLN C1055 " --> pdb=" O THR C 700 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N PHE C 702 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ILE C 704 " --> pdb=" O TYR C1051 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N TYR C1051 " --> pdb=" O ILE C 704 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL C 706 " --> pdb=" O VAL C1049 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL C1049 " --> pdb=" O VAL C 706 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR C 708 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU C1047 " --> pdb=" O THR C 708 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE C 710 " --> pdb=" O VAL C1045 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL C1045 " --> pdb=" O ILE C 710 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLY C1043 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA C1062 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE C1079 " --> pdb=" O ALA C1062 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 717 through 720 removed outlier: 4.381A pdb=" N LYS C 717 " --> pdb=" O LEU C 845 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1104 through 1109 removed outlier: 6.100A pdb=" N ALA C1071 " --> pdb=" O SER C1107 " (cutoff:3.500A) 1030 hydrogen bonds defined for protein. 2787 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: 7.33 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4972 1.32 - 1.45: 6444 1.45 - 1.57: 14481 1.57 - 1.69: 17 1.69 - 1.82: 139 Bond restraints: 26053 Sorted by residual: bond pdb=" C1 NAG B1203 " pdb=" O1 NAG B1203 " ideal model delta sigma weight residual 1.376 1.483 -0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C1 NAG B1204 " pdb=" O1 NAG B1204 " ideal model delta sigma weight residual 1.376 1.482 -0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" C1 NAG C1215 " pdb=" O1 NAG C1215 " ideal model delta sigma weight residual 1.376 1.481 -0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" C1 NAG A1211 " pdb=" O1 NAG A1211 " ideal model delta sigma weight residual 1.376 1.481 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C1 NAG C1213 " pdb=" O1 NAG C1213 " ideal model delta sigma weight residual 1.376 1.481 -0.105 2.00e-02 2.50e+03 2.75e+01 ... (remaining 26048 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 32074 2.00 - 4.01: 2813 4.01 - 6.01: 460 6.01 - 8.01: 132 8.01 - 10.02: 5 Bond angle restraints: 35484 Sorted by residual: angle pdb=" C LEU C 207 " pdb=" N PRO C 208 " pdb=" CA PRO C 208 " ideal model delta sigma weight residual 119.56 128.29 -8.73 1.02e+00 9.61e-01 7.33e+01 angle pdb=" C LEU C 845 " pdb=" N PRO C 846 " pdb=" CA PRO C 846 " ideal model delta sigma weight residual 119.66 125.70 -6.04 7.20e-01 1.93e+00 7.04e+01 angle pdb=" C PRO A 25 " pdb=" N PRO A 26 " pdb=" CA PRO A 26 " ideal model delta sigma weight residual 120.31 128.42 -8.11 9.80e-01 1.04e+00 6.84e+01 angle pdb=" C LEU A 207 " pdb=" N PRO A 208 " pdb=" CA PRO A 208 " ideal model delta sigma weight residual 120.21 128.06 -7.85 9.60e-01 1.09e+00 6.69e+01 angle pdb=" C THR A 775 " pdb=" N PRO A 776 " pdb=" CA PRO A 776 " ideal model delta sigma weight residual 119.66 125.45 -5.79 7.20e-01 1.93e+00 6.46e+01 ... (remaining 35479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 15529 17.96 - 35.92: 457 35.92 - 53.88: 100 53.88 - 71.84: 42 71.84 - 89.80: 17 Dihedral angle restraints: 16145 sinusoidal: 6935 harmonic: 9210 Sorted by residual: dihedral pdb=" CA THR B 583 " pdb=" C THR B 583 " pdb=" N PRO B 584 " pdb=" CA PRO B 584 " ideal model delta harmonic sigma weight residual 180.00 160.27 19.73 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA THR C 583 " pdb=" C THR C 583 " pdb=" N PRO C 584 " pdb=" CA PRO C 584 " ideal model delta harmonic sigma weight residual 180.00 162.96 17.04 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA SER C 367 " pdb=" C SER C 367 " pdb=" N PRO C 368 " pdb=" CA PRO C 368 " ideal model delta harmonic sigma weight residual 180.00 163.45 16.55 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 16142 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.987: 4139 0.987 - 1.975: 0 1.975 - 2.962: 0 2.962 - 3.949: 0 3.949 - 4.937: 1 Chirality restraints: 4140 Sorted by residual: chirality pdb=" C1 NAG A1206 " pdb=" ND2 ASN A 225 " pdb=" C2 NAG A1206 " pdb=" O5 NAG A1206 " both_signs ideal model delta sigma weight residual False -2.40 2.54 -4.94 2.00e-01 2.50e+01 6.09e+02 chirality pdb=" CG LEU C 233 " pdb=" CB LEU C 233 " pdb=" CD1 LEU C 233 " pdb=" CD2 LEU C 233 " both_signs ideal model delta sigma weight residual False -2.59 -2.97 0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" C2 NAG C1204 " pdb=" C1 NAG C1204 " pdb=" C3 NAG C1204 " pdb=" N2 NAG C1204 " both_signs ideal model delta sigma weight residual False -2.49 -2.85 0.35 2.00e-01 2.50e+01 3.13e+00 ... (remaining 4137 not shown) Planarity restraints: 4530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 437 " 0.039 2.00e-02 2.50e+03 2.11e-02 8.90e+00 pdb=" CG TYR A 437 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR A 437 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR A 437 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 437 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 437 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A 437 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 437 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 474 " 0.032 2.00e-02 2.50e+03 1.98e-02 6.86e+00 pdb=" CG PHE C 474 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE C 474 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE C 474 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE C 474 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 474 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE C 474 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 407 " 0.032 2.00e-02 2.50e+03 1.66e-02 5.51e+00 pdb=" CG TYR B 407 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR B 407 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 407 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR B 407 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR B 407 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 407 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 407 " 0.022 2.00e-02 2.50e+03 ... (remaining 4527 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 8712 2.85 - 3.36: 22932 3.36 - 3.87: 42590 3.87 - 4.39: 49334 4.39 - 4.90: 82283 Nonbonded interactions: 205851 Sorted by model distance: nonbonded pdb=" NZ LYS A 541 " pdb=" OD2 ASP A 558 " model vdw 2.336 3.120 nonbonded pdb=" OE2 GLU B 709 " pdb=" NZ LYS B1012 " model vdw 2.340 3.120 nonbonded pdb=" ND2 ASN B 590 " pdb=" OH TYR B 658 " model vdw 2.344 3.120 nonbonded pdb=" NZ LYS C 428 " pdb=" O PHE C 481 " model vdw 2.358 3.120 nonbonded pdb=" NZ LYS A 838 " pdb=" OD1 ASP C 558 " model vdw 2.384 3.120 ... (remaining 205846 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' and (resid 25 through 66 or resid 81 through 233 or resid 247 through \ 606 or resid 616 through 1203 or (resid 1204 and (name C1 or name C2 or name C3 \ or name C4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or \ name O4 or name O5 or name O6 or name O7 )) or resid 1205 through 1209 or (resi \ d 1210 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 or na \ me C7 or name C8 or name N2 or name O3 or name O4 or name O5 or name O6 or name \ O7 )) or resid 1211 or (resid 1212 and (name C1 or name C2 or name C3 or name C4 \ or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or \ name O5 or name O6 or name O7 )) or resid 1213 through 1215)) selection = (chain 'B' and (resid 25 through 66 or resid 81 through 233 or resid 247 through \ 606 or resid 616 through 1203 or (resid 1204 and (name C1 or name C2 or name C3 \ or name C4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or \ name O4 or name O5 or name O6 or name O7 )) or resid 1205 or (resid 1206 and (n \ ame C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name \ C8 or name N2 or name O3 or name O4 or name O5 or name O6 or name O7 )) or resi \ d 1207 through 1211 or (resid 1212 and (name C1 or name C2 or name C3 or name C4 \ or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or \ name O5 or name O6 or name O7 )) or resid 1213 through 1214 or (resid 1215 and \ (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or na \ me C8 or name N2 or name O3 or name O4 or name O5 or name O6 or name O7 )))) selection = (chain 'C' and (resid 25 through 233 or resid 247 through 811 or resid 838 throu \ gh 1205 or (resid 1206 and (name C1 or name C2 or name C3 or name C4 or name C5 \ or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or name O5 or \ name O6 or name O7 )) or resid 1207 through 1209 or (resid 1210 and (name C1 or \ name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or nam \ e N2 or name O3 or name O4 or name O5 or name O6 or name O7 )) or resid 1211 thr \ ough 1214 or (resid 1215 and (name C1 or name C2 or name C3 or name C4 or name C \ 5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 or name O5 o \ r name O6 or name O7 )))) } 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: 7.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.770 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 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 : 0.013 0.112 26058 Z= 0.699 Angle : 1.290 10.018 35499 Z= 0.864 Chirality : 0.111 4.937 4140 Planarity : 0.005 0.033 4525 Dihedral : 10.271 89.798 10225 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 1.05 % Allowed : 5.36 % Favored : 93.59 % Rotamer: Outliers : 0.14 % Allowed : 0.51 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.14), residues: 3137 helix: 0.33 (0.19), residues: 658 sheet: 0.70 (0.19), residues: 625 loop : -0.82 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 441 TYR 0.039 0.004 TYR A 437 PHE 0.032 0.003 PHE C 474 TRP 0.023 0.005 TRP A 64 HIS 0.005 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.01305 (26053) covalent geometry : angle 1.28953 (35484) hydrogen bonds : bond 0.16976 ( 997) hydrogen bonds : angle 7.94960 ( 2787) link_NAG-ASN : bond 0.05937 ( 5) link_NAG-ASN : angle 2.38664 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 503 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8635 (t) cc_final: 0.8309 (p) REVERT: A 167 LEU cc_start: 0.7189 (mt) cc_final: 0.6859 (mm) REVERT: A 191 TYR cc_start: 0.6777 (m-80) cc_final: 0.6492 (m-80) REVERT: A 387 ARG cc_start: 0.6332 (ttt180) cc_final: 0.5492 (mpt180) REVERT: A 443 SER cc_start: 0.7631 (p) cc_final: 0.7322 (p) REVERT: A 445 LEU cc_start: 0.6563 (tp) cc_final: 0.6069 (tp) REVERT: A 641 ASN cc_start: 0.7397 (t0) cc_final: 0.7104 (t0) REVERT: A 729 ASP cc_start: 0.7534 (p0) cc_final: 0.7137 (p0) REVERT: A 842 LEU cc_start: 0.8296 (tp) cc_final: 0.7935 (mt) REVERT: A 1122 TYR cc_start: 0.7719 (t80) cc_final: 0.7308 (m-10) REVERT: B 28 TYR cc_start: 0.7287 (m-80) cc_final: 0.7074 (m-80) REVERT: B 144 MET cc_start: 0.2138 (ttm) cc_final: 0.1578 (tpt) REVERT: C 63 THR cc_start: 0.7975 (m) cc_final: 0.7696 (p) REVERT: C 315 ASN cc_start: 0.5811 (OUTLIER) cc_final: 0.5464 (p0) REVERT: C 318 ASN cc_start: 0.7191 (m-40) cc_final: 0.6940 (t0) REVERT: C 353 TYR cc_start: 0.7035 (t80) cc_final: 0.6820 (t80) REVERT: C 411 ASP cc_start: 0.6882 (m-30) cc_final: 0.6433 (m-30) REVERT: C 448 PHE cc_start: 0.7845 (m-80) cc_final: 0.7615 (m-80) REVERT: C 492 TYR cc_start: 0.6662 (m-80) cc_final: 0.5858 (m-10) REVERT: C 1025 ASP cc_start: 0.7269 (m-30) cc_final: 0.7049 (m-30) outliers start: 4 outliers final: 1 residues processed: 507 average time/residue: 0.1935 time to fit residues: 148.3093 Evaluate side-chains 245 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 243 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain C residue 315 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS A 139 ASN A 198 HIS A 354 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 434 ASN A 490 GLN A 701 ASN A1085 HIS B 66 HIS B 693 ASN B1058 ASN C 187 ASN C 202 ASN C 266 ASN C 490 GLN C1032 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.154081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.099977 restraints weight = 38732.689| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.57 r_work: 0.3042 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26058 Z= 0.158 Angle : 0.656 11.035 35499 Z= 0.346 Chirality : 0.048 0.852 4140 Planarity : 0.004 0.049 4525 Dihedral : 5.739 51.664 4535 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.67 % Favored : 94.17 % Rotamer: Outliers : 1.19 % Allowed : 5.12 % Favored : 93.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.15), residues: 3137 helix: 1.64 (0.21), residues: 649 sheet: 0.66 (0.19), residues: 714 loop : -1.03 (0.15), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 341 TYR 0.026 0.002 TYR C 161 PHE 0.026 0.002 PHE B 159 TRP 0.009 0.001 TRP A 420 HIS 0.007 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00353 (26053) covalent geometry : angle 0.65053 (35484) hydrogen bonds : bond 0.05175 ( 997) hydrogen bonds : angle 5.89843 ( 2787) link_NAG-ASN : bond 0.00616 ( 5) link_NAG-ASN : angle 3.99811 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 288 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7936 (tp40) cc_final: 0.7595 (tm-30) REVERT: A 90 VAL cc_start: 0.8562 (t) cc_final: 0.7941 (p) REVERT: A 129 LYS cc_start: 0.7280 (mttt) cc_final: 0.7005 (mptt) REVERT: A 137 HIS cc_start: 0.4815 (OUTLIER) cc_final: 0.4472 (p-80) REVERT: A 162 VAL cc_start: 0.8151 (t) cc_final: 0.7763 (p) REVERT: A 191 TYR cc_start: 0.7111 (m-80) cc_final: 0.6845 (m-80) REVERT: A 349 TYR cc_start: 0.7760 (m-80) cc_final: 0.7302 (m-80) REVERT: A 380 TYR cc_start: 0.7990 (m-80) cc_final: 0.7746 (m-80) REVERT: A 434 ASN cc_start: 0.4851 (OUTLIER) cc_final: 0.3496 (p0) REVERT: A 476 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6172 (pp) REVERT: A 729 ASP cc_start: 0.8262 (p0) cc_final: 0.7892 (p0) REVERT: A 771 GLN cc_start: 0.8427 (mt0) cc_final: 0.8203 (mt0) REVERT: A 842 LEU cc_start: 0.8922 (tp) cc_final: 0.8317 (mt) REVERT: A 1122 TYR cc_start: 0.8097 (t80) cc_final: 0.7148 (m-10) REVERT: B 125 ASN cc_start: 0.7181 (p0) cc_final: 0.6968 (m-40) REVERT: B 136 TYR cc_start: 0.6653 (t80) cc_final: 0.6316 (t80) REVERT: B 144 MET cc_start: 0.1862 (ttm) cc_final: 0.1297 (tpt) REVERT: B 917 LYS cc_start: 0.8826 (mttt) cc_final: 0.8502 (mtmm) REVERT: B 1111 ASP cc_start: 0.8228 (p0) cc_final: 0.7874 (t0) REVERT: B 1128 GLU cc_start: 0.7581 (tp30) cc_final: 0.7277 (mm-30) REVERT: C 63 THR cc_start: 0.7790 (m) cc_final: 0.7366 (p) REVERT: C 102 ARG cc_start: 0.6415 (mmm-85) cc_final: 0.6134 (mtp85) REVERT: C 120 VAL cc_start: 0.7995 (t) cc_final: 0.7607 (m) REVERT: C 129 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7443 (mtpt) REVERT: C 318 ASN cc_start: 0.7028 (m-40) cc_final: 0.6776 (t0) REVERT: C 324 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7382 (tm-30) REVERT: C 341 ARG cc_start: 0.7573 (mtp-110) cc_final: 0.7323 (ttm110) REVERT: C 353 TYR cc_start: 0.7069 (t80) cc_final: 0.6714 (t80) REVERT: C 448 PHE cc_start: 0.8126 (m-80) cc_final: 0.7805 (m-80) REVERT: C 489 TYR cc_start: 0.3702 (OUTLIER) cc_final: 0.1705 (m-80) REVERT: C 566 LEU cc_start: 0.8535 (mp) cc_final: 0.8255 (mp) REVERT: C 576 PHE cc_start: 0.8600 (p90) cc_final: 0.8375 (p90) REVERT: C 919 GLN cc_start: 0.8178 (tm-30) cc_final: 0.7866 (tm-30) outliers start: 33 outliers final: 15 residues processed: 311 average time/residue: 0.1485 time to fit residues: 73.6066 Evaluate side-chains 230 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 210 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 HIS Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 729 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 39 optimal weight: 8.9990 chunk 181 optimal weight: 6.9990 chunk 163 optimal weight: 3.9990 chunk 253 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 chunk 295 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS A 139 ASN A 315 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 ASN A 885 GLN ** A1032 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 198 HIS B 639 HIS B 693 ASN B 994 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 266 ASN C 639 HIS C1082 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.152645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.098858 restraints weight = 38664.597| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.66 r_work: 0.2966 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 26058 Z= 0.194 Angle : 0.635 11.560 35499 Z= 0.330 Chirality : 0.047 0.632 4140 Planarity : 0.004 0.043 4525 Dihedral : 5.866 57.728 4533 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.44 % Favored : 93.37 % Rotamer: Outliers : 1.30 % Allowed : 7.15 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.15), residues: 3137 helix: 1.62 (0.21), residues: 667 sheet: 0.47 (0.18), residues: 739 loop : -1.22 (0.15), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 34 TYR 0.026 0.002 TYR B1051 PHE 0.028 0.002 PHE B 159 TRP 0.009 0.001 TRP B 617 HIS 0.013 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00454 (26053) covalent geometry : angle 0.63074 (35484) hydrogen bonds : bond 0.05077 ( 997) hydrogen bonds : angle 5.63741 ( 2787) link_NAG-ASN : bond 0.00392 ( 5) link_NAG-ASN : angle 3.81717 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 224 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8031 (tp40) cc_final: 0.7657 (tm-30) REVERT: A 81 ASN cc_start: 0.6180 (m-40) cc_final: 0.5963 (m-40) REVERT: A 271 ASP cc_start: 0.8172 (t0) cc_final: 0.7951 (m-30) REVERT: A 352 LEU cc_start: 0.8932 (mt) cc_final: 0.8699 (mm) REVERT: A 380 TYR cc_start: 0.8131 (m-80) cc_final: 0.7871 (m-80) REVERT: A 434 ASN cc_start: 0.5732 (m-40) cc_final: 0.4710 (p0) REVERT: A 437 TYR cc_start: 0.6705 (t80) cc_final: 0.6282 (t80) REVERT: A 729 ASP cc_start: 0.8314 (p0) cc_final: 0.7890 (p0) REVERT: A 900 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8772 (tt) REVERT: B 66 HIS cc_start: 0.6048 (p90) cc_final: 0.5814 (p-80) REVERT: B 129 LYS cc_start: 0.7934 (mttm) cc_final: 0.7563 (mtpp) REVERT: B 133 PHE cc_start: 0.7965 (m-10) cc_final: 0.7752 (m-10) REVERT: B 144 MET cc_start: 0.1829 (ttm) cc_final: 0.1369 (tpt) REVERT: B 1128 GLU cc_start: 0.7626 (tp30) cc_final: 0.7274 (mm-30) REVERT: C 63 THR cc_start: 0.7873 (m) cc_final: 0.7339 (p) REVERT: C 120 VAL cc_start: 0.7925 (t) cc_final: 0.7531 (m) REVERT: C 318 ASN cc_start: 0.7131 (m-40) cc_final: 0.6855 (t0) REVERT: C 322 PHE cc_start: 0.8118 (m-10) cc_final: 0.7917 (m-10) REVERT: C 324 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7358 (tm-30) REVERT: C 341 ARG cc_start: 0.7603 (mtp-110) cc_final: 0.7357 (ttm110) REVERT: C 448 PHE cc_start: 0.8164 (m-80) cc_final: 0.7770 (m-80) REVERT: C 489 TYR cc_start: 0.4190 (OUTLIER) cc_final: 0.2194 (m-80) REVERT: C 492 TYR cc_start: 0.6451 (m-80) cc_final: 0.5990 (m-10) REVERT: C 516 ASN cc_start: 0.8427 (t0) cc_final: 0.8194 (t0) REVERT: C 548 GLN cc_start: 0.7766 (mm-40) cc_final: 0.7474 (mm110) REVERT: C 566 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8254 (mp) REVERT: C 576 PHE cc_start: 0.8726 (p90) cc_final: 0.8509 (p90) REVERT: C 888 TYR cc_start: 0.7993 (m-10) cc_final: 0.7759 (m-10) outliers start: 36 outliers final: 19 residues processed: 251 average time/residue: 0.1394 time to fit residues: 57.2583 Evaluate side-chains 212 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 734 SER Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 952 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 337 TRP Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 729 ASP Chi-restraints excluded: chain C residue 1016 CYS Chi-restraints excluded: chain C residue 1125 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 313 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 218 optimal weight: 8.9990 chunk 174 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 126 optimal weight: 8.9990 chunk 176 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 HIS A 701 ASN ** A1032 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 587 ASN B 885 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1082 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.151327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.095189 restraints weight = 38714.265| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.32 r_work: 0.3014 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 26058 Z= 0.217 Angle : 0.630 11.616 35499 Z= 0.327 Chirality : 0.047 0.466 4140 Planarity : 0.004 0.043 4525 Dihedral : 6.001 48.576 4533 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.57 % Favored : 93.27 % Rotamer: Outliers : 1.59 % Allowed : 7.80 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.15), residues: 3137 helix: 1.75 (0.21), residues: 646 sheet: 0.28 (0.19), residues: 711 loop : -1.34 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 102 TYR 0.024 0.002 TYR B1051 PHE 0.022 0.002 PHE C 384 TRP 0.017 0.002 TRP B 870 HIS 0.005 0.001 HIS A 639 Details of bonding type rmsd covalent geometry : bond 0.00513 (26053) covalent geometry : angle 0.62450 (35484) hydrogen bonds : bond 0.04998 ( 997) hydrogen bonds : angle 5.55250 ( 2787) link_NAG-ASN : bond 0.00580 ( 5) link_NAG-ASN : angle 4.05839 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8050 (tp40) cc_final: 0.7741 (tp40) REVERT: A 129 LYS cc_start: 0.7363 (mttt) cc_final: 0.7013 (mtpt) REVERT: A 271 ASP cc_start: 0.8099 (t0) cc_final: 0.7883 (m-30) REVERT: A 437 TYR cc_start: 0.6846 (t80) cc_final: 0.6373 (t80) REVERT: A 440 PHE cc_start: 0.5400 (t80) cc_final: 0.5166 (t80) REVERT: A 446 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7277 (mtpp) REVERT: A 576 PHE cc_start: 0.7032 (p90) cc_final: 0.6792 (p90) REVERT: A 729 ASP cc_start: 0.8216 (p0) cc_final: 0.7796 (p0) REVERT: A 900 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8806 (tt) REVERT: B 52 GLN cc_start: 0.8281 (tp40) cc_final: 0.7940 (tp40) REVERT: B 129 LYS cc_start: 0.7865 (mttm) cc_final: 0.7517 (mtpp) REVERT: B 144 MET cc_start: 0.1670 (ttm) cc_final: 0.1325 (tpt) REVERT: B 1128 GLU cc_start: 0.7583 (tp30) cc_final: 0.7209 (mm-30) REVERT: C 63 THR cc_start: 0.7899 (m) cc_final: 0.7332 (p) REVERT: C 120 VAL cc_start: 0.7929 (t) cc_final: 0.7524 (m) REVERT: C 318 ASN cc_start: 0.7004 (m-40) cc_final: 0.6736 (t0) REVERT: C 324 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7330 (tm-30) REVERT: C 448 PHE cc_start: 0.8164 (m-80) cc_final: 0.7828 (m-80) REVERT: C 489 TYR cc_start: 0.4723 (OUTLIER) cc_final: 0.2526 (m-80) REVERT: C 492 TYR cc_start: 0.6585 (m-80) cc_final: 0.6109 (m-10) REVERT: C 516 ASN cc_start: 0.8419 (t0) cc_final: 0.8173 (t0) REVERT: C 566 LEU cc_start: 0.8574 (mp) cc_final: 0.8327 (mp) REVERT: C 888 TYR cc_start: 0.8011 (m-10) cc_final: 0.7663 (m-10) outliers start: 44 outliers final: 31 residues processed: 246 average time/residue: 0.1280 time to fit residues: 53.0848 Evaluate side-chains 215 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 734 SER Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 952 SER Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 969 ASP Chi-restraints excluded: chain B residue 1102 ASP Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 603 GLU Chi-restraints excluded: chain C residue 729 ASP Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 1016 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 186 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 245 optimal weight: 3.9990 chunk 273 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 309 optimal weight: 0.6980 chunk 213 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1032 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 338 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.152440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.099975 restraints weight = 38332.880| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.47 r_work: 0.3006 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26058 Z= 0.139 Angle : 0.563 9.324 35499 Z= 0.295 Chirality : 0.044 0.456 4140 Planarity : 0.004 0.042 4525 Dihedral : 5.613 47.765 4533 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.82 % Favored : 93.05 % Rotamer: Outliers : 1.59 % Allowed : 8.66 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.15), residues: 3137 helix: 1.88 (0.21), residues: 654 sheet: 0.19 (0.19), residues: 711 loop : -1.32 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 387 TYR 0.021 0.001 TYR B1051 PHE 0.027 0.001 PHE B 159 TRP 0.009 0.001 TRP B 870 HIS 0.003 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00316 (26053) covalent geometry : angle 0.55881 (35484) hydrogen bonds : bond 0.04379 ( 997) hydrogen bonds : angle 5.35140 ( 2787) link_NAG-ASN : bond 0.00488 ( 5) link_NAG-ASN : angle 3.41865 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 198 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7374 (mttt) cc_final: 0.7073 (mtpt) REVERT: A 271 ASP cc_start: 0.8150 (t0) cc_final: 0.7929 (m-30) REVERT: A 437 TYR cc_start: 0.6862 (t80) cc_final: 0.6466 (t80) REVERT: A 446 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7283 (mtpp) REVERT: A 505 PRO cc_start: 0.7780 (Cg_endo) cc_final: 0.7475 (Cg_exo) REVERT: A 729 ASP cc_start: 0.8272 (p0) cc_final: 0.7846 (p0) REVERT: A 757 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7899 (tt0) REVERT: A 792 ASP cc_start: 0.6259 (OUTLIER) cc_final: 0.5647 (p0) REVERT: A 900 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8693 (tt) REVERT: B 129 LYS cc_start: 0.7910 (mttm) cc_final: 0.7544 (mtpp) REVERT: B 135 PHE cc_start: 0.6502 (OUTLIER) cc_final: 0.6125 (m-80) REVERT: B 144 MET cc_start: 0.1659 (ttm) cc_final: 0.1406 (tpt) REVERT: B 1128 GLU cc_start: 0.7472 (tp30) cc_final: 0.7177 (mm-30) REVERT: C 63 THR cc_start: 0.7869 (m) cc_final: 0.7374 (p) REVERT: C 120 VAL cc_start: 0.7914 (t) cc_final: 0.7527 (m) REVERT: C 318 ASN cc_start: 0.6957 (m-40) cc_final: 0.6733 (t0) REVERT: C 324 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7404 (tm-30) REVERT: C 448 PHE cc_start: 0.8108 (m-80) cc_final: 0.7802 (m-80) REVERT: C 489 TYR cc_start: 0.4587 (OUTLIER) cc_final: 0.2441 (m-80) REVERT: C 492 TYR cc_start: 0.6570 (m-80) cc_final: 0.6136 (m-10) REVERT: C 516 ASN cc_start: 0.8428 (t0) cc_final: 0.8166 (t0) REVERT: C 566 LEU cc_start: 0.8676 (mp) cc_final: 0.8450 (mp) REVERT: C 888 TYR cc_start: 0.8056 (m-10) cc_final: 0.7783 (m-10) outliers start: 44 outliers final: 30 residues processed: 232 average time/residue: 0.1252 time to fit residues: 48.6276 Evaluate side-chains 219 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 952 SER Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 384 PHE Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 724 MET Chi-restraints excluded: chain C residue 885 GLN Chi-restraints excluded: chain C residue 1016 CYS Chi-restraints excluded: chain C residue 1125 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 130 optimal weight: 5.9990 chunk 156 optimal weight: 0.6980 chunk 187 optimal weight: 0.6980 chunk 311 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 232 optimal weight: 2.9990 chunk 268 optimal weight: 9.9990 chunk 293 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 287 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 ASN A1055 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 898 ASN ** C1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.152097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.098130 restraints weight = 38611.520| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.64 r_work: 0.2987 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26058 Z= 0.152 Angle : 0.557 9.295 35499 Z= 0.292 Chirality : 0.045 0.418 4140 Planarity : 0.004 0.046 4525 Dihedral : 5.481 49.229 4533 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.76 % Favored : 93.11 % Rotamer: Outliers : 2.02 % Allowed : 8.81 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.15), residues: 3137 helix: 1.96 (0.21), residues: 652 sheet: 0.16 (0.19), residues: 681 loop : -1.35 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 303 TYR 0.022 0.001 TYR B1051 PHE 0.023 0.002 PHE B 159 TRP 0.010 0.001 TRP B 870 HIS 0.003 0.001 HIS B1042 Details of bonding type rmsd covalent geometry : bond 0.00351 (26053) covalent geometry : angle 0.55343 (35484) hydrogen bonds : bond 0.04362 ( 997) hydrogen bonds : angle 5.29131 ( 2787) link_NAG-ASN : bond 0.00558 ( 5) link_NAG-ASN : angle 3.22806 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 199 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6315 (m-40) cc_final: 0.6040 (t0) REVERT: A 129 LYS cc_start: 0.7387 (mttt) cc_final: 0.7088 (mtpt) REVERT: A 271 ASP cc_start: 0.8183 (t0) cc_final: 0.7921 (m-30) REVERT: A 437 TYR cc_start: 0.6789 (t80) cc_final: 0.6545 (t80) REVERT: A 446 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7347 (mtpp) REVERT: A 451 ASP cc_start: 0.6529 (t0) cc_final: 0.6225 (t70) REVERT: A 505 PRO cc_start: 0.7762 (Cg_endo) cc_final: 0.7526 (Cg_exo) REVERT: A 729 ASP cc_start: 0.8307 (p0) cc_final: 0.7869 (p0) REVERT: A 757 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7936 (tt0) REVERT: A 792 ASP cc_start: 0.6255 (OUTLIER) cc_final: 0.5648 (p0) REVERT: A 900 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8643 (tt) REVERT: B 52 GLN cc_start: 0.8346 (tp40) cc_final: 0.8071 (tp40) REVERT: B 129 LYS cc_start: 0.7927 (mttm) cc_final: 0.7532 (mtpp) REVERT: B 135 PHE cc_start: 0.6517 (OUTLIER) cc_final: 0.6101 (m-80) REVERT: B 144 MET cc_start: 0.1514 (ttm) cc_final: 0.1312 (tpt) REVERT: B 1128 GLU cc_start: 0.7430 (tp30) cc_final: 0.7152 (mm-30) REVERT: C 63 THR cc_start: 0.7901 (m) cc_final: 0.7351 (p) REVERT: C 120 VAL cc_start: 0.7923 (t) cc_final: 0.7533 (m) REVERT: C 318 ASN cc_start: 0.6963 (m-40) cc_final: 0.6741 (t0) REVERT: C 324 GLU cc_start: 0.7533 (tm-30) cc_final: 0.7301 (tm-30) REVERT: C 448 PHE cc_start: 0.8096 (m-80) cc_final: 0.7862 (m-80) REVERT: C 489 TYR cc_start: 0.4703 (OUTLIER) cc_final: 0.2476 (m-80) REVERT: C 492 TYR cc_start: 0.6608 (m-80) cc_final: 0.6158 (m-10) REVERT: C 516 ASN cc_start: 0.8470 (t0) cc_final: 0.8206 (t0) REVERT: C 566 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8500 (mp) outliers start: 56 outliers final: 36 residues processed: 243 average time/residue: 0.1294 time to fit residues: 52.2159 Evaluate side-chains 222 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 180 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 952 SER Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1090 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 969 ASP Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 337 TRP Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 384 PHE Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 603 GLU Chi-restraints excluded: chain C residue 724 MET Chi-restraints excluded: chain C residue 729 ASP Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 885 GLN Chi-restraints excluded: chain C residue 1016 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 254 optimal weight: 5.9990 chunk 256 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 249 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 279 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 287 optimal weight: 0.5980 chunk 301 optimal weight: 0.9980 chunk 236 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.152908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.100469 restraints weight = 38575.797| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.54 r_work: 0.2999 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26058 Z= 0.128 Angle : 0.538 10.291 35499 Z= 0.280 Chirality : 0.044 0.380 4140 Planarity : 0.004 0.043 4525 Dihedral : 5.271 49.344 4533 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.11 % Favored : 92.76 % Rotamer: Outliers : 1.62 % Allowed : 9.71 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.15), residues: 3137 helix: 2.02 (0.21), residues: 660 sheet: 0.17 (0.19), residues: 675 loop : -1.34 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 181 TYR 0.020 0.001 TYR B1051 PHE 0.029 0.001 PHE B 159 TRP 0.008 0.001 TRP C 64 HIS 0.004 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00289 (26053) covalent geometry : angle 0.53464 (35484) hydrogen bonds : bond 0.04105 ( 997) hydrogen bonds : angle 5.19978 ( 2787) link_NAG-ASN : bond 0.00478 ( 5) link_NAG-ASN : angle 2.97140 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 191 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6401 (m-40) cc_final: 0.6118 (t0) REVERT: A 129 LYS cc_start: 0.7322 (mttt) cc_final: 0.6973 (mtpt) REVERT: A 271 ASP cc_start: 0.8182 (t0) cc_final: 0.7923 (m-30) REVERT: A 437 TYR cc_start: 0.6806 (t80) cc_final: 0.6593 (t80) REVERT: A 446 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7331 (mtpp) REVERT: A 451 ASP cc_start: 0.6562 (t0) cc_final: 0.6274 (t70) REVERT: A 505 PRO cc_start: 0.7755 (Cg_endo) cc_final: 0.7528 (Cg_exo) REVERT: A 729 ASP cc_start: 0.8323 (p0) cc_final: 0.7893 (p0) REVERT: A 757 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7915 (tt0) REVERT: A 792 ASP cc_start: 0.6197 (OUTLIER) cc_final: 0.5560 (p0) REVERT: B 52 GLN cc_start: 0.8355 (tp40) cc_final: 0.8041 (tp40) REVERT: B 129 LYS cc_start: 0.7936 (mttm) cc_final: 0.7536 (mtpp) REVERT: B 135 PHE cc_start: 0.6435 (OUTLIER) cc_final: 0.6047 (m-80) REVERT: B 1128 GLU cc_start: 0.7424 (tp30) cc_final: 0.7130 (mm-30) REVERT: C 63 THR cc_start: 0.7891 (m) cc_final: 0.7401 (p) REVERT: C 120 VAL cc_start: 0.7891 (t) cc_final: 0.7484 (m) REVERT: C 341 ARG cc_start: 0.7494 (mtp-110) cc_final: 0.7283 (ttm-80) REVERT: C 448 PHE cc_start: 0.8038 (m-80) cc_final: 0.7739 (m-80) REVERT: C 489 TYR cc_start: 0.4684 (OUTLIER) cc_final: 0.2449 (m-80) REVERT: C 492 TYR cc_start: 0.6601 (m-80) cc_final: 0.6104 (m-10) REVERT: C 516 ASN cc_start: 0.8479 (t0) cc_final: 0.8119 (t0) REVERT: C 566 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8488 (mp) outliers start: 45 outliers final: 28 residues processed: 229 average time/residue: 0.1298 time to fit residues: 49.4737 Evaluate side-chains 209 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 1090 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 337 TRP Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 724 MET Chi-restraints excluded: chain C residue 729 ASP Chi-restraints excluded: chain C residue 1016 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 144 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 255 optimal weight: 7.9990 chunk 153 optimal weight: 0.9980 chunk 170 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 285 optimal weight: 9.9990 chunk 203 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 243 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1055 GLN B 693 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 597 GLN ** C1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.150301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.096409 restraints weight = 38630.727| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.61 r_work: 0.2950 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 26058 Z= 0.240 Angle : 0.623 9.324 35499 Z= 0.322 Chirality : 0.047 0.382 4140 Planarity : 0.004 0.040 4525 Dihedral : 5.912 51.417 4533 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.71 % Favored : 92.16 % Rotamer: Outliers : 1.73 % Allowed : 10.00 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.15), residues: 3137 helix: 1.82 (0.21), residues: 654 sheet: 0.08 (0.19), residues: 676 loop : -1.46 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 303 TYR 0.024 0.002 TYR B1051 PHE 0.028 0.002 PHE C 384 TRP 0.014 0.002 TRP B 870 HIS 0.005 0.001 HIS B1042 Details of bonding type rmsd covalent geometry : bond 0.00570 (26053) covalent geometry : angle 0.61936 (35484) hydrogen bonds : bond 0.04981 ( 997) hydrogen bonds : angle 5.46350 ( 2787) link_NAG-ASN : bond 0.00467 ( 5) link_NAG-ASN : angle 3.20650 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 188 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6390 (m-40) cc_final: 0.6186 (t0) REVERT: A 129 LYS cc_start: 0.7270 (mttt) cc_final: 0.6903 (mtpt) REVERT: A 168 MET cc_start: 0.6698 (mpp) cc_final: 0.6228 (mpp) REVERT: A 271 ASP cc_start: 0.8212 (t0) cc_final: 0.7897 (m-30) REVERT: A 446 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7359 (mtpp) REVERT: A 505 PRO cc_start: 0.7630 (Cg_endo) cc_final: 0.7424 (Cg_exo) REVERT: A 729 ASP cc_start: 0.8385 (p0) cc_final: 0.7958 (p0) REVERT: A 792 ASP cc_start: 0.6498 (OUTLIER) cc_final: 0.5923 (p0) REVERT: A 900 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.8824 (tt) REVERT: B 129 LYS cc_start: 0.7903 (mttm) cc_final: 0.7540 (mtpp) REVERT: B 135 PHE cc_start: 0.6549 (OUTLIER) cc_final: 0.6004 (m-80) REVERT: B 1128 GLU cc_start: 0.7371 (tp30) cc_final: 0.7055 (mm-30) REVERT: C 63 THR cc_start: 0.7890 (m) cc_final: 0.7309 (p) REVERT: C 120 VAL cc_start: 0.7891 (t) cc_final: 0.7490 (m) REVERT: C 341 ARG cc_start: 0.7507 (mtp-110) cc_final: 0.7279 (ttm-80) REVERT: C 448 PHE cc_start: 0.8075 (m-80) cc_final: 0.7844 (m-80) REVERT: C 489 TYR cc_start: 0.5007 (OUTLIER) cc_final: 0.2716 (m-80) REVERT: C 492 TYR cc_start: 0.6686 (m-80) cc_final: 0.6246 (m-10) REVERT: C 494 VAL cc_start: 0.8436 (m) cc_final: 0.8206 (p) REVERT: C 516 ASN cc_start: 0.8409 (t0) cc_final: 0.8127 (t0) REVERT: C 566 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8499 (mp) outliers start: 48 outliers final: 38 residues processed: 224 average time/residue: 0.1184 time to fit residues: 44.8664 Evaluate side-chains 222 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 178 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 952 SER Chi-restraints excluded: chain A residue 1090 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 693 ASN Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 969 ASP Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 337 TRP Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 603 GLU Chi-restraints excluded: chain C residue 724 MET Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 885 GLN Chi-restraints excluded: chain C residue 898 ASN Chi-restraints excluded: chain C residue 1016 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 87 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 260 optimal weight: 0.9990 chunk 268 optimal weight: 10.0000 chunk 267 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 310 optimal weight: 5.9990 chunk 214 optimal weight: 0.9990 chunk 293 optimal weight: 3.9990 chunk 307 optimal weight: 0.3980 chunk 131 optimal weight: 0.8980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1055 GLN B 693 ASN C 121 ASN ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 701 ASN C1085 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.152132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.098896 restraints weight = 38458.203| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.61 r_work: 0.2990 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26058 Z= 0.138 Angle : 0.553 9.293 35499 Z= 0.288 Chirality : 0.044 0.357 4140 Planarity : 0.004 0.040 4525 Dihedral : 5.551 50.688 4533 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.08 % Favored : 92.80 % Rotamer: Outliers : 1.77 % Allowed : 10.14 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.15), residues: 3137 helix: 1.95 (0.21), residues: 660 sheet: -0.00 (0.19), residues: 669 loop : -1.42 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 303 TYR 0.021 0.001 TYR C1122 PHE 0.031 0.001 PHE C 384 TRP 0.012 0.001 TRP A 143 HIS 0.004 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00313 (26053) covalent geometry : angle 0.54958 (35484) hydrogen bonds : bond 0.04277 ( 997) hydrogen bonds : angle 5.28507 ( 2787) link_NAG-ASN : bond 0.00531 ( 5) link_NAG-ASN : angle 2.89334 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 190 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6427 (m-40) cc_final: 0.6056 (t0) REVERT: A 129 LYS cc_start: 0.7309 (mttt) cc_final: 0.7096 (mtpp) REVERT: A 168 MET cc_start: 0.6694 (mpp) cc_final: 0.6244 (mpp) REVERT: A 271 ASP cc_start: 0.8123 (t0) cc_final: 0.7827 (m-30) REVERT: A 437 TYR cc_start: 0.6812 (t80) cc_final: 0.6532 (t80) REVERT: A 446 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7400 (mtpp) REVERT: A 505 PRO cc_start: 0.7566 (Cg_endo) cc_final: 0.7360 (Cg_exo) REVERT: A 710 ILE cc_start: 0.9393 (OUTLIER) cc_final: 0.9063 (mm) REVERT: A 729 ASP cc_start: 0.8385 (p0) cc_final: 0.7965 (p0) REVERT: A 757 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7934 (tt0) REVERT: A 792 ASP cc_start: 0.6260 (OUTLIER) cc_final: 0.5865 (p0) REVERT: A 900 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8669 (tt) REVERT: B 52 GLN cc_start: 0.8333 (tp40) cc_final: 0.8086 (tp40) REVERT: B 129 LYS cc_start: 0.7927 (mttm) cc_final: 0.7552 (mtpp) REVERT: B 135 PHE cc_start: 0.6499 (OUTLIER) cc_final: 0.6049 (m-80) REVERT: B 1128 GLU cc_start: 0.7371 (tp30) cc_final: 0.7051 (mm-30) REVERT: C 63 THR cc_start: 0.7877 (m) cc_final: 0.7331 (p) REVERT: C 120 VAL cc_start: 0.7846 (t) cc_final: 0.7480 (m) REVERT: C 341 ARG cc_start: 0.7457 (mtp-110) cc_final: 0.7229 (ttm-80) REVERT: C 448 PHE cc_start: 0.7999 (m-80) cc_final: 0.7734 (m-80) REVERT: C 489 TYR cc_start: 0.4819 (OUTLIER) cc_final: 0.2542 (m-80) REVERT: C 492 TYR cc_start: 0.6686 (m-80) cc_final: 0.6207 (m-10) REVERT: C 494 VAL cc_start: 0.8416 (m) cc_final: 0.8175 (p) REVERT: C 516 ASN cc_start: 0.8367 (t0) cc_final: 0.8083 (t0) REVERT: C 566 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8525 (mp) outliers start: 49 outliers final: 32 residues processed: 230 average time/residue: 0.1298 time to fit residues: 50.2853 Evaluate side-chains 222 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 183 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 1090 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 693 ASN Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 969 ASP Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 337 TRP Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 729 ASP Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 885 GLN Chi-restraints excluded: chain C residue 1016 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 191 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 213 optimal weight: 0.1980 chunk 190 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 31 optimal weight: 0.0010 chunk 164 optimal weight: 6.9990 chunk 300 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 ASN ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 701 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.152319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.098999 restraints weight = 38286.900| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.59 r_work: 0.2996 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26058 Z= 0.137 Angle : 0.549 9.281 35499 Z= 0.286 Chirality : 0.044 0.327 4140 Planarity : 0.004 0.040 4525 Dihedral : 5.349 50.602 4533 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.20 % Favored : 92.67 % Rotamer: Outliers : 1.52 % Allowed : 10.36 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.15), residues: 3137 helix: 2.02 (0.21), residues: 658 sheet: -0.01 (0.19), residues: 679 loop : -1.43 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 303 TYR 0.021 0.001 TYR C1051 PHE 0.030 0.001 PHE B 159 TRP 0.011 0.001 TRP A 143 HIS 0.005 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00314 (26053) covalent geometry : angle 0.54626 (35484) hydrogen bonds : bond 0.04176 ( 997) hydrogen bonds : angle 5.23496 ( 2787) link_NAG-ASN : bond 0.00473 ( 5) link_NAG-ASN : angle 2.74817 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.6466 (m-40) cc_final: 0.6093 (t0) REVERT: A 129 LYS cc_start: 0.7308 (mttt) cc_final: 0.6942 (mtpt) REVERT: A 168 MET cc_start: 0.6683 (mpp) cc_final: 0.6228 (mpp) REVERT: A 271 ASP cc_start: 0.8118 (t0) cc_final: 0.7826 (m-30) REVERT: A 446 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7353 (mtpp) REVERT: A 710 ILE cc_start: 0.9389 (OUTLIER) cc_final: 0.9063 (mm) REVERT: A 729 ASP cc_start: 0.8334 (p0) cc_final: 0.7910 (p0) REVERT: A 757 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7946 (tt0) REVERT: A 792 ASP cc_start: 0.6214 (OUTLIER) cc_final: 0.5576 (p0) REVERT: A 900 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8654 (tt) REVERT: B 52 GLN cc_start: 0.8327 (tp40) cc_final: 0.8080 (tp40) REVERT: B 129 LYS cc_start: 0.7940 (mttm) cc_final: 0.7536 (mtpp) REVERT: B 135 PHE cc_start: 0.6505 (OUTLIER) cc_final: 0.6049 (m-80) REVERT: B 1128 GLU cc_start: 0.7382 (tp30) cc_final: 0.7047 (mm-30) REVERT: C 63 THR cc_start: 0.7874 (m) cc_final: 0.7351 (p) REVERT: C 120 VAL cc_start: 0.7863 (t) cc_final: 0.7507 (m) REVERT: C 341 ARG cc_start: 0.7425 (mtp-110) cc_final: 0.7193 (ttm-80) REVERT: C 448 PHE cc_start: 0.7996 (m-80) cc_final: 0.7705 (m-80) REVERT: C 489 TYR cc_start: 0.4753 (OUTLIER) cc_final: 0.2493 (m-80) REVERT: C 492 TYR cc_start: 0.6670 (m-80) cc_final: 0.6170 (m-10) REVERT: C 494 VAL cc_start: 0.8393 (m) cc_final: 0.8157 (p) REVERT: C 516 ASN cc_start: 0.8352 (t0) cc_final: 0.8066 (t0) REVERT: C 566 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8542 (mp) outliers start: 42 outliers final: 32 residues processed: 223 average time/residue: 0.1274 time to fit residues: 47.1165 Evaluate side-chains 222 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 183 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 446 LYS Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 1090 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 693 ASN Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain B residue 893 ILE Chi-restraints excluded: chain B residue 969 ASP Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 168 MET Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 337 TRP Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 416 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 729 ASP Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 885 GLN Chi-restraints excluded: chain C residue 1016 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 19 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 210 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 282 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 197 optimal weight: 0.7980 chunk 202 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 ASN ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 597 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.151254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.098787 restraints weight = 38120.364| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.40 r_work: 0.2975 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26058 Z= 0.121 Angle : 0.538 9.277 35499 Z= 0.281 Chirality : 0.044 0.315 4140 Planarity : 0.004 0.062 4525 Dihedral : 5.177 50.496 4533 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.20 % Favored : 92.67 % Rotamer: Outliers : 1.52 % Allowed : 10.43 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.15), residues: 3137 helix: 2.06 (0.21), residues: 660 sheet: 0.01 (0.19), residues: 675 loop : -1.42 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 303 TYR 0.023 0.001 TYR A1122 PHE 0.029 0.001 PHE B 159 TRP 0.012 0.001 TRP A 143 HIS 0.005 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00269 (26053) covalent geometry : angle 0.53516 (35484) hydrogen bonds : bond 0.03992 ( 997) hydrogen bonds : angle 5.19043 ( 2787) link_NAG-ASN : bond 0.00489 ( 5) link_NAG-ASN : angle 2.62771 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6962.78 seconds wall clock time: 119 minutes 54.65 seconds (7194.65 seconds total)