Starting phenix.real_space_refine on Sun Jun 22 07:09:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fu8_29455/06_2025/8fu8_29455_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fu8_29455/06_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_29455/06_2025/8fu8_29455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fu8_29455/06_2025/8fu8_29455.map" model { file = "/net/cci-nas-00/data/ceres_data/8fu8_29455/06_2025/8fu8_29455_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fu8_29455/06_2025/8fu8_29455_neut.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.65, per 1000 atoms: 0.61 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: 5.86 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 4.11 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: 10.78 Time building geometry restraints manager: 7.04 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 1130 or resid 1201 through 1203 or (resid 1204 and (na \ me 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 (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 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 na \ me 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 throu \ gh 1215)) selection = (chain 'B' and (resid 25 through 66 or resid 81 through 233 or resid 247 through \ 606 or resid 616 through 1130 or resid 1201 through 1203 or (resid 1204 and (na \ me 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 (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 na \ me O6 or name O7 )) or resid 1207 through 1211 or (resid 1212 and (name C1 or na \ me 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 throu \ gh 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 name 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 1130 or resid 1201 through 1205 or (resid 1206 and (name C1 or name C2 or nam \ e C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O \ 3 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 o \ r name C7 or name C8 or name N2 or name O3 or name O4 or name O5 or name O6 or n \ ame O7 )) or resid 1211 through 1214 or (resid 1215 and (name C1 or name C2 or n \ ame 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 )))) } 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: 4.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 1.210 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 59.400 Find NCS groups from input model: 2.160 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.290 ------------------------------------------------------------------------------- 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 : 1.90 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.023 0.005 TRP A 64 HIS 0.005 0.001 HIS A 137 PHE 0.032 0.003 PHE C 474 TYR 0.039 0.004 TYR A 437 ARG 0.005 0.000 ARG A 441 Details of bonding type rmsd link_NAG-ASN : bond 0.05937 ( 5) link_NAG-ASN : angle 2.38664 ( 15) hydrogen bonds : bond 0.16976 ( 997) hydrogen bonds : angle 7.94960 ( 2787) covalent geometry : bond 0.01305 (26053) covalent geometry : angle 1.28953 (35484) *********************** 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 : 4.221 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 90 VAL cc_start: 0.8635 (t) cc_final: 0.8310 (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: 0.6454 (m-80) REVERT: A 387 ARG cc_start: 0.6332 (ttt180) cc_final: 0.5492 (mpt180) REVERT: A 401 LYS cc_start: 0.7271 (pttt) cc_final: 0.7071 (ptmm) REVERT: A 435 TYR cc_start: 0.6479 (m-80) cc_final: 0.6234 (m-80) REVERT: A 443 SER cc_start: 0.7631 (p) cc_final: 0.7323 (p) REVERT: A 445 LEU cc_start: 0.6563 (tp) cc_final: 0.6071 (tp) REVERT: A 641 ASN cc_start: 0.7397 (t0) cc_final: 0.7105 (t0) REVERT: A 729 ASP cc_start: 0.7534 (p0) cc_final: 0.7138 (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: 0.7075 (m-80) REVERT: B 144 MET cc_start: 0.2138 (ttm) cc_final: 0.1574 (tpt) REVERT: C 63 THR cc_start: 0.7975 (m) cc_final: 0.7695 (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: 0.6819 (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: 0.5490 time to fit residues: 424.5573 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 : 6.380 ------------------------------------------------------------------------------- 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 265 optimal weight: 0.9990 chunk 238 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 161 optimal weight: 0.6980 chunk 127 optimal weight: 0.8980 chunk 246 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 286 optimal weight: 8.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 209 GLN A 354 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 ASN ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 ASN A1085 HIS B 66 HIS B 693 ASN B1058 ASN C 187 ASN C 266 ASN C 490 GLN C1032 HIS ** C1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.155528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.099939 restraints weight = 38661.105| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.34 r_work: 0.3092 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26058 Z= 0.148 Angle : 0.649 13.068 35499 Z= 0.345 Chirality : 0.049 1.064 4140 Planarity : 0.004 0.047 4525 Dihedral : 5.656 51.420 4535 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.61 % Favored : 94.23 % Rotamer: Outliers : 1.12 % Allowed : 5.23 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.15), residues: 3137 helix: 1.70 (0.21), residues: 649 sheet: 0.67 (0.18), residues: 715 loop : -1.00 (0.15), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 420 HIS 0.008 0.001 HIS B 137 PHE 0.025 0.002 PHE B 159 TYR 0.026 0.002 TYR C 161 ARG 0.007 0.001 ARG A 341 Details of bonding type rmsd link_NAG-ASN : bond 0.00566 ( 5) link_NAG-ASN : angle 4.28441 ( 15) hydrogen bonds : bond 0.05434 ( 997) hydrogen bonds : angle 6.01217 ( 2787) covalent geometry : bond 0.00321 (26053) covalent geometry : angle 0.64346 (35484) *********************** 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: 31 poor density : 290 time to evaluate : 3.064 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: 0.7892 (tp40) cc_final: 0.7565 (tm-30) REVERT: A 81 ASN cc_start: 0.6267 (m-40) cc_final: 0.5998 (m-40) REVERT: A 90 VAL cc_start: 0.8632 (t) cc_final: 0.8022 (p) REVERT: A 129 LYS cc_start: 0.7230 (mttt) cc_final: 0.6934 (mptt) REVERT: A 137 HIS cc_start: 0.4670 (OUTLIER) cc_final: 0.4405 (p-80) REVERT: A 162 VAL cc_start: 0.8153 (t) cc_final: 0.7751 (p) REVERT: A 191 TYR cc_start: 0.7044 (m-80) cc_final: 0.6837 (m-80) REVERT: A 435 TYR cc_start: 0.6473 (m-80) cc_final: 0.6195 (m-80) REVERT: A 641 ASN cc_start: 0.8031 (t0) cc_final: 0.7650 (t0) REVERT: A 729 ASP cc_start: 0.8187 (p0) cc_final: 0.7797 (p0) REVERT: A 771 GLN cc_start: 0.8376 (mt0) cc_final: 0.8156 (mt0) REVERT: A 842 LEU cc_start: 0.8873 (tp) cc_final: 0.8308 (mt) REVERT: A 1122 TYR cc_start: 0.7979 (t80) cc_final: 0.7073 (m-10) REVERT: B 125 ASN cc_start: 0.7171 (p0) cc_final: 0.6942 (m-40) REVERT: B 144 MET cc_start: 0.2056 (ttm) cc_final: 0.1462 (tpt) REVERT: B 917 LYS cc_start: 0.8833 (mttt) cc_final: 0.8507 (mtmm) REVERT: B 972 GLU cc_start: 0.8532 (mp0) cc_final: 0.8273 (mp0) REVERT: B 1111 ASP cc_start: 0.8154 (p0) cc_final: 0.7849 (t0) REVERT: B 1128 GLU cc_start: 0.7563 (tp30) cc_final: 0.7291 (mm-30) REVERT: C 63 THR cc_start: 0.7779 (m) cc_final: 0.7373 (p) REVERT: C 120 VAL cc_start: 0.7957 (t) cc_final: 0.7626 (m) REVERT: C 318 ASN cc_start: 0.6948 (m-40) cc_final: 0.6704 (t0) REVERT: C 324 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7362 (tm-30) REVERT: C 448 PHE cc_start: 0.8086 (m-80) cc_final: 0.7784 (m-80) REVERT: C 489 TYR cc_start: 0.3710 (OUTLIER) cc_final: 0.1750 (m-80) REVERT: C 492 TYR cc_start: 0.6782 (m-80) cc_final: 0.6039 (m-10) REVERT: C 566 LEU cc_start: 0.8533 (mp) cc_final: 0.8246 (mp) REVERT: C 576 PHE cc_start: 0.8580 (p90) cc_final: 0.8379 (p90) REVERT: C 919 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7841 (tm-30) outliers start: 31 outliers final: 14 residues processed: 310 average time/residue: 0.3612 time to fit residues: 179.5272 Evaluate side-chains 229 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 213 time to evaluate : 2.608 ------------------------------------------------------------------------------- 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 B residue 66 HIS 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 629 THR Chi-restraints excluded: chain B residue 840 ASN 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 113 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 301 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 32 optimal weight: 0.0570 chunk 79 optimal weight: 1.9990 chunk 255 optimal weight: 4.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 HIS A 209 GLN A 315 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 HIS A 701 ASN A 885 GLN ** A1032 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 HIS B 587 ASN B 639 HIS B 885 GLN B 994 GLN C 125 ASN C 202 ASN C 266 ASN C 639 HIS ** C1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.151750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.095553 restraints weight = 38601.224| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.30 r_work: 0.3011 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 26058 Z= 0.224 Angle : 0.657 11.570 35499 Z= 0.343 Chirality : 0.047 0.434 4140 Planarity : 0.004 0.045 4525 Dihedral : 6.028 49.355 4533 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.60 % Favored : 93.21 % Rotamer: Outliers : 1.44 % Allowed : 7.15 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3137 helix: 1.52 (0.21), residues: 666 sheet: 0.49 (0.18), residues: 731 loop : -1.24 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 870 HIS 0.020 0.002 HIS B 66 PHE 0.028 0.002 PHE A 148 TYR 0.028 0.002 TYR B1051 ARG 0.008 0.001 ARG C 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00509 ( 5) link_NAG-ASN : angle 3.12399 ( 15) hydrogen bonds : bond 0.05268 ( 997) hydrogen bonds : angle 5.71667 ( 2787) covalent geometry : bond 0.00530 (26053) covalent geometry : angle 0.65389 (35484) *********************** 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 266 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 226 time to evaluate : 2.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7973 (tp40) cc_final: 0.7604 (tm-30) REVERT: A 58 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.8079 (m-10) REVERT: A 81 ASN cc_start: 0.6191 (m-40) cc_final: 0.5969 (m-40) REVERT: A 225 ASN cc_start: 0.6474 (t0) cc_final: 0.6179 (m-40) REVERT: A 271 ASP cc_start: 0.8035 (t0) cc_final: 0.7786 (m-30) REVERT: A 352 LEU cc_start: 0.8940 (mt) cc_final: 0.8682 (mm) REVERT: A 387 ARG cc_start: 0.6216 (ttt180) cc_final: 0.5416 (mpt180) REVERT: A 435 TYR cc_start: 0.6603 (m-80) cc_final: 0.6375 (m-80) REVERT: A 437 TYR cc_start: 0.6761 (t80) cc_final: 0.6264 (t80) REVERT: A 576 PHE cc_start: 0.6850 (p90) cc_final: 0.6624 (p90) REVERT: A 701 ASN cc_start: 0.9287 (OUTLIER) cc_final: 0.9066 (t0) REVERT: A 729 ASP cc_start: 0.8233 (p0) cc_final: 0.7808 (p0) REVERT: A 792 ASP cc_start: 0.6388 (OUTLIER) cc_final: 0.5804 (p0) REVERT: A 900 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8822 (tt) REVERT: B 144 MET cc_start: 0.1836 (ttm) cc_final: 0.1322 (tpt) REVERT: B 376 PHE cc_start: 0.6637 (m-80) cc_final: 0.6421 (m-80) REVERT: B 1128 GLU cc_start: 0.7624 (tp30) cc_final: 0.7267 (mm-30) REVERT: C 63 THR cc_start: 0.7879 (m) cc_final: 0.7294 (p) REVERT: C 120 VAL cc_start: 0.7904 (t) cc_final: 0.7522 (m) REVERT: C 318 ASN cc_start: 0.7096 (m-40) cc_final: 0.6807 (t0) REVERT: C 324 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7294 (tm-30) REVERT: C 448 PHE cc_start: 0.8150 (m-80) cc_final: 0.7788 (m-80) REVERT: C 489 TYR cc_start: 0.4252 (OUTLIER) cc_final: 0.2213 (m-80) REVERT: C 516 ASN cc_start: 0.8384 (t0) cc_final: 0.8159 (t0) REVERT: C 548 GLN cc_start: 0.7683 (mm-40) cc_final: 0.7366 (mm110) REVERT: C 566 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8229 (mp) REVERT: C 576 PHE cc_start: 0.8653 (p90) cc_final: 0.8438 (p90) REVERT: C 888 TYR cc_start: 0.7893 (m-10) cc_final: 0.7658 (m-10) outliers start: 40 outliers final: 25 residues processed: 257 average time/residue: 0.3457 time to fit residues: 145.1356 Evaluate side-chains 221 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 701 ASN Chi-restraints excluded: chain A residue 734 SER 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 B residue 29 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 224 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 1016 CYS Chi-restraints excluded: chain B residue 1084 THR Chi-restraints excluded: chain C residue 125 ASN 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 194 optimal weight: 3.9990 chunk 144 optimal weight: 20.0000 chunk 180 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 242 optimal weight: 7.9990 chunk 181 optimal weight: 2.9990 chunk 173 optimal weight: 0.8980 chunk 202 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 ** A1032 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1082 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 = 0.3960 r_free = 0.3960 target = 0.151748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.095889 restraints weight = 38545.943| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.30 r_work: 0.3012 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26058 Z= 0.186 Angle : 0.607 9.344 35499 Z= 0.317 Chirality : 0.046 0.349 4140 Planarity : 0.004 0.043 4525 Dihedral : 5.790 48.326 4533 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.73 % Favored : 93.11 % Rotamer: Outliers : 1.62 % Allowed : 7.69 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 3137 helix: 1.65 (0.21), residues: 662 sheet: 0.35 (0.18), residues: 733 loop : -1.35 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 870 HIS 0.004 0.001 HIS C1048 PHE 0.022 0.002 PHE C 384 TYR 0.023 0.002 TYR B1051 ARG 0.007 0.000 ARG A 438 Details of bonding type rmsd link_NAG-ASN : bond 0.00464 ( 5) link_NAG-ASN : angle 2.89086 ( 15) hydrogen bonds : bond 0.04802 ( 997) hydrogen bonds : angle 5.53913 ( 2787) covalent geometry : bond 0.00437 (26053) covalent geometry : angle 0.60458 (35484) *********************** 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 252 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 207 time to evaluate : 2.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8032 (tp40) cc_final: 0.7730 (tp40) REVERT: A 58 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7978 (m-10) REVERT: A 129 LYS cc_start: 0.7348 (mttt) cc_final: 0.7086 (mtpt) REVERT: A 271 ASP cc_start: 0.8063 (t0) cc_final: 0.7847 (m-30) REVERT: A 352 LEU cc_start: 0.8966 (mt) cc_final: 0.8763 (mm) REVERT: A 387 ARG cc_start: 0.6208 (ttt180) cc_final: 0.5417 (mpt180) REVERT: A 401 LYS cc_start: 0.7627 (mmtp) cc_final: 0.7399 (mmtp) REVERT: A 437 TYR cc_start: 0.6823 (t80) cc_final: 0.6361 (t80) REVERT: A 446 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7270 (mtpp) REVERT: A 576 PHE cc_start: 0.6873 (p90) cc_final: 0.6655 (p90) REVERT: A 701 ASN cc_start: 0.9190 (OUTLIER) cc_final: 0.8698 (t0) REVERT: A 729 ASP cc_start: 0.8226 (p0) cc_final: 0.7807 (p0) REVERT: B 52 GLN cc_start: 0.8324 (tp40) cc_final: 0.8006 (tp40) REVERT: B 144 MET cc_start: 0.1755 (ttm) cc_final: 0.1373 (tpt) REVERT: B 168 MET cc_start: 0.5471 (mmm) cc_final: 0.5243 (mmm) REVERT: B 1128 GLU cc_start: 0.7623 (tp30) cc_final: 0.7258 (mm-30) REVERT: C 63 THR cc_start: 0.7860 (m) cc_final: 0.7289 (p) REVERT: C 120 VAL cc_start: 0.7888 (t) cc_final: 0.7496 (m) REVERT: C 318 ASN cc_start: 0.6962 (m-40) cc_final: 0.6717 (t0) REVERT: C 324 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7314 (tm-30) REVERT: C 448 PHE cc_start: 0.8142 (m-80) cc_final: 0.7787 (m-80) REVERT: C 489 TYR cc_start: 0.4589 (OUTLIER) cc_final: 0.2470 (m-80) REVERT: C 516 ASN cc_start: 0.8407 (t0) cc_final: 0.8167 (t0) REVERT: C 566 LEU cc_start: 0.8568 (mp) cc_final: 0.8319 (mp) REVERT: C 888 TYR cc_start: 0.7970 (m-10) cc_final: 0.7717 (m-10) outliers start: 45 outliers final: 29 residues processed: 240 average time/residue: 0.3409 time to fit residues: 135.9440 Evaluate side-chains 221 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 2.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE 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 629 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 701 ASN Chi-restraints excluded: chain A residue 734 SER Chi-restraints excluded: chain A residue 839 PHE 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 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 1102 ASP Chi-restraints excluded: chain C residue 58 PHE 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 509 CYS 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 1016 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 170 optimal weight: 0.7980 chunk 257 optimal weight: 0.8980 chunk 209 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 302 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 206 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 245 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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** A 701 ASN A1032 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 338 ASN C 898 ASN ** C1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.152425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.099563 restraints weight = 38515.766| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.58 r_work: 0.2990 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26058 Z= 0.146 Angle : 0.572 9.338 35499 Z= 0.299 Chirality : 0.045 0.524 4140 Planarity : 0.004 0.042 4525 Dihedral : 5.580 49.585 4533 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.63 % Favored : 93.24 % Rotamer: Outliers : 1.44 % Allowed : 8.70 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.15), residues: 3137 helix: 1.85 (0.21), residues: 656 sheet: 0.24 (0.19), residues: 719 loop : -1.32 (0.15), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 870 HIS 0.003 0.001 HIS B 137 PHE 0.028 0.002 PHE B 159 TYR 0.021 0.001 TYR B1051 ARG 0.007 0.000 ARG A 438 Details of bonding type rmsd link_NAG-ASN : bond 0.00646 ( 5) link_NAG-ASN : angle 3.72904 ( 15) hydrogen bonds : bond 0.04415 ( 997) hydrogen bonds : angle 5.38969 ( 2787) covalent geometry : bond 0.00332 (26053) covalent geometry : angle 0.56678 (35484) *********************** 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 247 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 207 time to evaluate : 2.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.8087 (m-80) REVERT: A 129 LYS cc_start: 0.7476 (mttt) cc_final: 0.7218 (mtpp) REVERT: A 271 ASP cc_start: 0.8107 (t0) cc_final: 0.7899 (m-30) REVERT: A 352 LEU cc_start: 0.8984 (mt) cc_final: 0.8770 (mm) REVERT: A 387 ARG cc_start: 0.6178 (ttt180) cc_final: 0.5601 (mpt180) REVERT: A 390 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7206 (mp0) REVERT: A 401 LYS cc_start: 0.7649 (mmtp) cc_final: 0.7434 (mmtp) REVERT: A 437 TYR cc_start: 0.6822 (t80) cc_final: 0.6271 (t80) REVERT: A 438 ARG cc_start: 0.7363 (mmt90) cc_final: 0.7143 (mmt90) REVERT: A 446 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7247 (mtpp) REVERT: A 576 PHE cc_start: 0.6925 (p90) cc_final: 0.6690 (p90) REVERT: A 729 ASP cc_start: 0.8287 (p0) cc_final: 0.7857 (p0) REVERT: A 757 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7935 (tt0) REVERT: A 900 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8752 (tt) REVERT: B 144 MET cc_start: 0.1797 (ttm) cc_final: 0.1496 (tpt) REVERT: B 168 MET cc_start: 0.5554 (mmm) cc_final: 0.5325 (mmm) REVERT: B 376 PHE cc_start: 0.6755 (m-80) cc_final: 0.6416 (m-80) REVERT: B 1128 GLU cc_start: 0.7585 (tp30) cc_final: 0.7212 (mm-30) REVERT: C 63 THR cc_start: 0.7880 (m) cc_final: 0.7327 (p) REVERT: C 120 VAL cc_start: 0.7930 (t) cc_final: 0.7542 (m) REVERT: C 318 ASN cc_start: 0.6976 (m-40) cc_final: 0.6745 (t0) REVERT: C 324 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7342 (tm-30) REVERT: C 448 PHE cc_start: 0.8114 (m-80) cc_final: 0.7787 (m-80) REVERT: C 489 TYR cc_start: 0.4524 (OUTLIER) cc_final: 0.2353 (m-80) REVERT: C 516 ASN cc_start: 0.8455 (t0) cc_final: 0.8213 (t0) REVERT: C 566 LEU cc_start: 0.8637 (mp) cc_final: 0.8410 (mp) REVERT: C 778 ILE cc_start: 0.8324 (tp) cc_final: 0.8109 (pt) REVERT: C 888 TYR cc_start: 0.8062 (m-10) cc_final: 0.7796 (m-10) outliers start: 40 outliers final: 27 residues processed: 239 average time/residue: 0.3371 time to fit residues: 134.7648 Evaluate side-chains 212 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 181 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE 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 641 ASN Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 900 LEU 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 199 THR Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 587 ASN 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 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 454 THR Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 724 MET Chi-restraints excluded: chain C residue 885 GLN Chi-restraints excluded: chain C residue 1016 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 173 optimal weight: 6.9990 chunk 305 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 270 optimal weight: 0.7980 chunk 167 optimal weight: 7.9990 chunk 48 optimal weight: 0.0570 chunk 135 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 314 optimal weight: 0.3980 chunk 103 optimal weight: 0.6980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 701 ASN C1085 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.154056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.101540 restraints weight = 38528.773| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.59 r_work: 0.3029 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26058 Z= 0.104 Angle : 0.523 9.344 35499 Z= 0.275 Chirality : 0.043 0.461 4140 Planarity : 0.004 0.045 4525 Dihedral : 5.095 45.786 4533 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.79 % Favored : 93.08 % Rotamer: Outliers : 1.41 % Allowed : 9.17 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.15), residues: 3137 helix: 2.13 (0.21), residues: 651 sheet: 0.30 (0.19), residues: 702 loop : -1.26 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 337 HIS 0.004 0.000 HIS B 137 PHE 0.023 0.001 PHE B 159 TYR 0.020 0.001 TYR B1051 ARG 0.007 0.000 ARG A 438 Details of bonding type rmsd link_NAG-ASN : bond 0.00902 ( 5) link_NAG-ASN : angle 3.39994 ( 15) hydrogen bonds : bond 0.03765 ( 997) hydrogen bonds : angle 5.12255 ( 2787) covalent geometry : bond 0.00220 (26053) covalent geometry : angle 0.51861 (35484) *********************** 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 256 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 2.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.6422 (t) cc_final: 0.6181 (m) REVERT: A 129 LYS cc_start: 0.7490 (mttt) cc_final: 0.7125 (mtpt) REVERT: A 271 ASP cc_start: 0.8100 (t0) cc_final: 0.7889 (m-30) REVERT: A 352 LEU cc_start: 0.8939 (mt) cc_final: 0.8693 (mm) REVERT: A 387 ARG cc_start: 0.6204 (ttt180) cc_final: 0.5496 (mpt180) REVERT: A 401 LYS cc_start: 0.7657 (mmtp) cc_final: 0.7439 (mmtp) REVERT: A 437 TYR cc_start: 0.6784 (t80) cc_final: 0.6443 (t80) REVERT: A 446 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7244 (mtpp) REVERT: A 451 ASP cc_start: 0.6427 (t0) cc_final: 0.6162 (t70) REVERT: A 505 PRO cc_start: 0.7780 (Cg_endo) cc_final: 0.7502 (Cg_exo) REVERT: A 701 ASN cc_start: 0.9248 (OUTLIER) cc_final: 0.8927 (t0) REVERT: A 729 ASP cc_start: 0.8275 (p0) cc_final: 0.7864 (p0) REVERT: A 900 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8659 (tt) REVERT: B 52 GLN cc_start: 0.8383 (tp40) cc_final: 0.8086 (tp40) REVERT: B 144 MET cc_start: 0.1786 (ttm) cc_final: 0.1500 (tpt) REVERT: B 1128 GLU cc_start: 0.7477 (tp30) cc_final: 0.7156 (mm-30) REVERT: C 63 THR cc_start: 0.7862 (m) cc_final: 0.7360 (p) REVERT: C 120 VAL cc_start: 0.7895 (t) cc_final: 0.7513 (m) REVERT: C 324 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7404 (tm-30) REVERT: C 448 PHE cc_start: 0.8056 (m-80) cc_final: 0.7741 (m-80) REVERT: C 489 TYR cc_start: 0.4405 (OUTLIER) cc_final: 0.2287 (m-80) REVERT: C 492 TYR cc_start: 0.6690 (m-80) cc_final: 0.6255 (m-10) REVERT: C 516 ASN cc_start: 0.8441 (t0) cc_final: 0.8182 (t0) REVERT: C 566 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8474 (mp) REVERT: C 576 PHE cc_start: 0.8633 (p90) cc_final: 0.8354 (p90) REVERT: C 778 ILE cc_start: 0.8247 (tp) cc_final: 0.8010 (pt) REVERT: C 888 TYR cc_start: 0.8015 (m-10) cc_final: 0.7770 (m-10) outliers start: 39 outliers final: 23 residues processed: 245 average time/residue: 0.3395 time to fit residues: 137.0537 Evaluate side-chains 211 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 3.059 ------------------------------------------------------------------------------- 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 446 LYS Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 701 ASN 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 70 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 531 THR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 337 TRP Chi-restraints excluded: chain C residue 345 CYS 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 489 TYR Chi-restraints excluded: chain C residue 509 CYS Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 701 ASN Chi-restraints excluded: chain C residue 729 ASP 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 6 optimal weight: 2.9990 chunk 261 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 235 optimal weight: 30.0000 chunk 170 optimal weight: 1.9990 chunk 216 optimal weight: 10.0000 chunk 174 optimal weight: 4.9990 chunk 27 optimal weight: 0.0570 chunk 285 optimal weight: 4.9990 chunk 160 optimal weight: 0.5980 chunk 30 optimal weight: 9.9990 overall best weight: 2.1304 ------------------------------------------------------------------------------- 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 587 ASN B1103 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 597 GLN C 701 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.151039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.097685 restraints weight = 38601.648| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.63 r_work: 0.2939 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 26058 Z= 0.193 Angle : 0.590 9.831 35499 Z= 0.307 Chirality : 0.046 0.433 4140 Planarity : 0.004 0.040 4525 Dihedral : 5.522 48.616 4533 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.17 % Favored : 92.70 % Rotamer: Outliers : 1.88 % Allowed : 9.71 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.15), residues: 3137 helix: 1.97 (0.21), residues: 654 sheet: 0.18 (0.19), residues: 674 loop : -1.33 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 870 HIS 0.005 0.001 HIS C1048 PHE 0.028 0.002 PHE B 159 TYR 0.023 0.002 TYR C1051 ARG 0.005 0.000 ARG C 303 Details of bonding type rmsd link_NAG-ASN : bond 0.00612 ( 5) link_NAG-ASN : angle 3.06189 ( 15) hydrogen bonds : bond 0.04594 ( 997) hydrogen bonds : angle 5.31119 ( 2787) covalent geometry : bond 0.00456 (26053) covalent geometry : angle 0.58666 (35484) *********************** 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 246 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 194 time to evaluate : 2.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.7972 (m-80) REVERT: A 129 LYS cc_start: 0.7477 (mttt) cc_final: 0.7106 (mtpt) REVERT: A 230 GLN cc_start: 0.7711 (tt0) cc_final: 0.7449 (tt0) REVERT: A 271 ASP cc_start: 0.8172 (t0) cc_final: 0.7913 (m-30) REVERT: A 352 LEU cc_start: 0.8940 (mt) cc_final: 0.8707 (mm) REVERT: A 437 TYR cc_start: 0.6716 (t80) cc_final: 0.6334 (t80) REVERT: A 446 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7305 (mtpp) REVERT: A 505 PRO cc_start: 0.7811 (Cg_endo) cc_final: 0.7551 (Cg_exo) REVERT: A 729 ASP cc_start: 0.8354 (p0) cc_final: 0.7921 (p0) REVERT: A 792 ASP cc_start: 0.6267 (OUTLIER) cc_final: 0.5609 (p0) REVERT: A 900 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8843 (tt) REVERT: B 144 MET cc_start: 0.1624 (ttm) cc_final: 0.1392 (tpt) REVERT: B 1128 GLU cc_start: 0.7438 (tp30) cc_final: 0.7159 (mm-30) REVERT: C 63 THR cc_start: 0.7853 (m) cc_final: 0.7268 (p) REVERT: C 120 VAL cc_start: 0.7907 (t) cc_final: 0.7552 (m) REVERT: C 168 MET cc_start: 0.6700 (mpp) cc_final: 0.6321 (mpp) REVERT: C 324 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7263 (tm-30) REVERT: C 448 PHE cc_start: 0.8043 (m-80) cc_final: 0.7753 (m-80) REVERT: C 489 TYR cc_start: 0.4617 (OUTLIER) cc_final: 0.2443 (m-80) REVERT: C 516 ASN cc_start: 0.8463 (t0) cc_final: 0.8197 (t0) REVERT: C 566 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8489 (mp) outliers start: 52 outliers final: 33 residues processed: 235 average time/residue: 0.3211 time to fit residues: 126.9093 Evaluate side-chains 216 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 58 PHE 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 B residue 29 THR Chi-restraints excluded: chain B residue 70 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 227 THR 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 384 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 509 CYS Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 569 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 1016 CYS Chi-restraints excluded: chain C residue 1082 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 99 optimal weight: 0.8980 chunk 304 optimal weight: 0.0050 chunk 115 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 212 optimal weight: 3.9990 chunk 286 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 309 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- 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 ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 597 GLN C1103 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.152924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.099811 restraints weight = 38397.001| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.49 r_work: 0.3004 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26058 Z= 0.121 Angle : 0.533 9.436 35499 Z= 0.279 Chirality : 0.044 0.394 4140 Planarity : 0.004 0.040 4525 Dihedral : 5.131 47.528 4533 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.11 % Favored : 92.76 % Rotamer: Outliers : 1.55 % Allowed : 10.07 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.15), residues: 3137 helix: 2.12 (0.21), residues: 654 sheet: 0.17 (0.19), residues: 676 loop : -1.30 (0.15), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 64 HIS 0.004 0.001 HIS B 137 PHE 0.026 0.001 PHE B 159 TYR 0.020 0.001 TYR B1051 ARG 0.006 0.000 ARG C 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00634 ( 5) link_NAG-ASN : angle 2.82068 ( 15) hydrogen bonds : bond 0.03991 ( 997) hydrogen bonds : angle 5.15397 ( 2787) covalent geometry : bond 0.00270 (26053) covalent geometry : angle 0.52978 (35484) *********************** 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 235 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 192 time to evaluate : 2.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7424 (mttt) cc_final: 0.6989 (mtpt) REVERT: A 230 GLN cc_start: 0.7478 (tt0) cc_final: 0.6884 (tp40) REVERT: A 271 ASP cc_start: 0.8121 (t0) cc_final: 0.7873 (m-30) REVERT: A 352 LEU cc_start: 0.8927 (mt) cc_final: 0.8709 (mm) REVERT: A 446 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7332 (mtpp) REVERT: A 451 ASP cc_start: 0.6412 (t0) cc_final: 0.6203 (t70) REVERT: A 505 PRO cc_start: 0.7700 (Cg_endo) cc_final: 0.7451 (Cg_exo) REVERT: A 729 ASP cc_start: 0.8299 (p0) cc_final: 0.7860 (p0) REVERT: A 792 ASP cc_start: 0.6078 (OUTLIER) cc_final: 0.5417 (p0) REVERT: A 900 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8664 (tt) REVERT: B 52 GLN cc_start: 0.8365 (tp40) cc_final: 0.8100 (tp40) REVERT: B 144 MET cc_start: 0.1650 (ttm) cc_final: 0.1437 (tpt) REVERT: B 168 MET cc_start: 0.5273 (mmm) cc_final: 0.5047 (mmm) REVERT: B 1128 GLU cc_start: 0.7417 (tp30) cc_final: 0.7125 (mm-30) REVERT: C 63 THR cc_start: 0.7810 (m) cc_final: 0.7322 (p) REVERT: C 120 VAL cc_start: 0.7881 (t) cc_final: 0.7531 (m) REVERT: C 168 MET cc_start: 0.6733 (mpp) cc_final: 0.6349 (mpp) REVERT: C 448 PHE cc_start: 0.8008 (m-80) cc_final: 0.7782 (m-80) REVERT: C 489 TYR cc_start: 0.4577 (OUTLIER) cc_final: 0.2378 (m-80) REVERT: C 492 TYR cc_start: 0.6719 (m-80) cc_final: 0.6320 (m-10) REVERT: C 516 ASN cc_start: 0.8418 (t0) cc_final: 0.8064 (t0) REVERT: C 566 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8477 (mp) REVERT: C 674 GLN cc_start: 0.6943 (mp10) cc_final: 0.6668 (pm20) outliers start: 43 outliers final: 27 residues processed: 227 average time/residue: 0.3412 time to fit residues: 131.5185 Evaluate side-chains 213 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 2.931 ------------------------------------------------------------------------------- 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 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 B residue 29 THR Chi-restraints excluded: chain B residue 70 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 707 THR 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 369 THR Chi-restraints excluded: chain C residue 384 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 509 CYS Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 729 ASP Chi-restraints excluded: chain C residue 1016 CYS Chi-restraints excluded: chain C residue 1082 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 258 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 259 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 209 optimal weight: 0.0570 chunk 40 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 251 optimal weight: 0.0570 chunk 232 optimal weight: 7.9990 overall best weight: 2.0222 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.151071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.097249 restraints weight = 38760.336| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.49 r_work: 0.2976 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 26058 Z= 0.186 Angle : 0.579 9.857 35499 Z= 0.301 Chirality : 0.046 0.361 4140 Planarity : 0.004 0.038 4525 Dihedral : 5.455 49.916 4533 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.49 % Favored : 92.38 % Rotamer: Outliers : 1.66 % Allowed : 10.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 3137 helix: 2.00 (0.21), residues: 654 sheet: 0.05 (0.19), residues: 667 loop : -1.37 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 870 HIS 0.005 0.001 HIS B 137 PHE 0.023 0.002 PHE B 159 TYR 0.025 0.002 TYR B 136 ARG 0.005 0.000 ARG B 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00578 ( 5) link_NAG-ASN : angle 2.77267 ( 15) hydrogen bonds : bond 0.04565 ( 997) hydrogen bonds : angle 5.29800 ( 2787) covalent geometry : bond 0.00438 (26053) covalent geometry : angle 0.57643 (35484) *********************** 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 230 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 184 time to evaluate : 2.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.8001 (m-80) REVERT: A 129 LYS cc_start: 0.7332 (mttt) cc_final: 0.7049 (mtpp) REVERT: A 168 MET cc_start: 0.6694 (mpp) cc_final: 0.6240 (mpp) REVERT: A 271 ASP cc_start: 0.8116 (t0) cc_final: 0.7868 (m-30) REVERT: A 352 LEU cc_start: 0.8944 (mt) cc_final: 0.8732 (mm) REVERT: A 446 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7312 (mtpp) REVERT: A 451 ASP cc_start: 0.6538 (t0) cc_final: 0.6306 (t70) REVERT: A 505 PRO cc_start: 0.7583 (Cg_endo) cc_final: 0.7356 (Cg_exo) REVERT: A 729 ASP cc_start: 0.8321 (p0) cc_final: 0.7900 (p0) REVERT: A 792 ASP cc_start: 0.6252 (OUTLIER) cc_final: 0.5849 (p0) REVERT: A 900 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8866 (tt) REVERT: B 52 GLN cc_start: 0.8364 (tp40) cc_final: 0.8092 (tp40) REVERT: B 168 MET cc_start: 0.5354 (mmm) cc_final: 0.5125 (mmm) REVERT: B 1128 GLU cc_start: 0.7357 (tp30) cc_final: 0.7049 (mm-30) REVERT: C 63 THR cc_start: 0.7860 (m) cc_final: 0.7300 (p) REVERT: C 120 VAL cc_start: 0.7887 (t) cc_final: 0.7547 (m) REVERT: C 168 MET cc_start: 0.6967 (mpp) cc_final: 0.6633 (mpp) REVERT: C 448 PHE cc_start: 0.8009 (m-80) cc_final: 0.7733 (m-80) REVERT: C 489 TYR cc_start: 0.4666 (OUTLIER) cc_final: 0.2416 (m-80) REVERT: C 516 ASN cc_start: 0.8349 (t0) cc_final: 0.8066 (t0) REVERT: C 566 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8460 (mp) REVERT: C 674 GLN cc_start: 0.7050 (mp10) cc_final: 0.6815 (pm20) REVERT: C 905 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8678 (mttp) outliers start: 46 outliers final: 33 residues processed: 220 average time/residue: 0.3607 time to fit residues: 134.5382 Evaluate side-chains 213 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 58 PHE 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 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 B residue 29 THR Chi-restraints excluded: chain B residue 70 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 707 THR Chi-restraints excluded: chain B residue 840 ASN Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 227 THR 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 384 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 509 CYS Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 569 LEU 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 885 GLN Chi-restraints excluded: chain C residue 898 ASN Chi-restraints excluded: chain C residue 905 LYS Chi-restraints excluded: chain C residue 1016 CYS Chi-restraints excluded: chain C residue 1082 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 16 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 239 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 230 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN A 156 ASN A 372 ASN B 693 ASN C 121 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.151543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.097665 restraints weight = 38412.883| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.63 r_work: 0.2983 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26058 Z= 0.164 Angle : 0.562 10.144 35499 Z= 0.293 Chirality : 0.045 0.344 4140 Planarity : 0.004 0.039 4525 Dihedral : 5.435 50.154 4533 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.27 % Favored : 92.60 % Rotamer: Outliers : 1.59 % Allowed : 10.39 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.15), residues: 3137 helix: 2.05 (0.21), residues: 652 sheet: 0.02 (0.19), residues: 679 loop : -1.40 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 143 HIS 0.004 0.001 HIS B 137 PHE 0.029 0.002 PHE B 159 TYR 0.021 0.001 TYR B1051 ARG 0.008 0.000 ARG B 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00568 ( 5) link_NAG-ASN : angle 2.67936 ( 15) hydrogen bonds : bond 0.04350 ( 997) hydrogen bonds : angle 5.27525 ( 2787) covalent geometry : bond 0.00384 (26053) covalent geometry : angle 0.55961 (35484) ********************** 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 226 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 182 time to evaluate : 2.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7334 (mttt) cc_final: 0.7080 (mtpp) REVERT: A 168 MET cc_start: 0.6673 (mpp) cc_final: 0.6188 (mpp) REVERT: A 271 ASP cc_start: 0.8103 (t0) cc_final: 0.7846 (m-30) REVERT: A 446 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7332 (mtpp) REVERT: A 505 PRO cc_start: 0.7625 (Cg_endo) cc_final: 0.7393 (Cg_exo) REVERT: A 576 PHE cc_start: 0.7053 (p90) cc_final: 0.6789 (p90) REVERT: A 729 ASP cc_start: 0.8346 (p0) cc_final: 0.7931 (p0) REVERT: A 792 ASP cc_start: 0.6257 (OUTLIER) cc_final: 0.5617 (p0) REVERT: A 900 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8790 (tt) REVERT: B 52 GLN cc_start: 0.8354 (tp40) cc_final: 0.8081 (tp40) REVERT: B 168 MET cc_start: 0.5381 (mmm) cc_final: 0.5177 (mmm) REVERT: B 1128 GLU cc_start: 0.7367 (tp30) cc_final: 0.7048 (mm-30) REVERT: C 63 THR cc_start: 0.7793 (m) cc_final: 0.7239 (p) REVERT: C 120 VAL cc_start: 0.7905 (t) cc_final: 0.7618 (m) REVERT: C 168 MET cc_start: 0.6995 (mpp) cc_final: 0.6652 (mpp) REVERT: C 448 PHE cc_start: 0.7976 (m-80) cc_final: 0.7748 (m-80) REVERT: C 489 TYR cc_start: 0.4644 (OUTLIER) cc_final: 0.2358 (m-80) REVERT: C 516 ASN cc_start: 0.8329 (t0) cc_final: 0.8060 (t0) REVERT: C 566 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8476 (mp) REVERT: C 674 GLN cc_start: 0.7030 (mp10) cc_final: 0.6798 (pm20) REVERT: C 905 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8661 (mttp) outliers start: 44 outliers final: 32 residues processed: 217 average time/residue: 0.3390 time to fit residues: 122.5221 Evaluate side-chains 213 residues out of total 2771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 175 time to evaluate : 2.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR 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 B residue 29 THR Chi-restraints excluded: chain B residue 70 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 693 ASN Chi-restraints excluded: chain B residue 707 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 231 THR Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 384 PHE Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 509 CYS Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 569 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 905 LYS Chi-restraints excluded: chain C residue 1016 CYS Chi-restraints excluded: chain C residue 1082 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 184 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 42 optimal weight: 9.9990 chunk 146 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 209 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 250 optimal weight: 0.0770 chunk 71 optimal weight: 0.0170 chunk 277 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN B 693 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.152520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.099964 restraints weight = 38466.218| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.50 r_work: 0.3001 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26058 Z= 0.125 Angle : 0.540 9.854 35499 Z= 0.282 Chirality : 0.044 0.331 4140 Planarity : 0.004 0.062 4525 Dihedral : 5.252 49.868 4533 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.27 % Favored : 92.60 % Rotamer: Outliers : 1.48 % Allowed : 10.36 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 3137 helix: 2.12 (0.21), residues: 654 sheet: 0.04 (0.19), residues: 675 loop : -1.36 (0.15), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 143 HIS 0.004 0.001 HIS B 137 PHE 0.030 0.001 PHE B 159 TYR 0.025 0.001 TYR B 136 ARG 0.005 0.000 ARG B 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00582 ( 5) link_NAG-ASN : angle 2.56808 ( 15) hydrogen bonds : bond 0.04066 ( 997) hydrogen bonds : angle 5.22251 ( 2787) covalent geometry : bond 0.00280 (26053) covalent geometry : angle 0.53722 (35484) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18101.21 seconds wall clock time: 313 minutes 24.19 seconds (18804.19 seconds total)