Starting phenix.real_space_refine on Sat Jul 4 18:52:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8h15_34425/07_2026/8h15_34425.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h15_34425/07_2026/8h15_34425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14182 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h15_34425/07_2026/8h15_34425.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h15_34425/07_2026/8h15_34425.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8h15_34425/07_2026/8h15_34425.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8h15_34425/07_2026/8h15_34425.cif" model { file = "/net/cci-nas-00/data/ceres_data/8h15_34425/07_2026/8h15_34425.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h15_34425/07_2026/8h15_34425.cif" } resolution = 3.14182 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 120 5.16 5 C 14563 2.51 5 N 3757 2.21 5 O 4373 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 126 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22813 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 968, 7565 Classifications: {'peptide': 968} Link IDs: {'PTRANS': 43, 'TRANS': 924} Chain breaks: 12 Chain: "B" Number of atoms: 7480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 958, 7480 Classifications: {'peptide': 958} Link IDs: {'PTRANS': 42, 'TRANS': 915} Chain breaks: 11 Chain: "C" Number of atoms: 7516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 962, 7516 Classifications: {'peptide': 962} Link IDs: {'PTRANS': 43, 'TRANS': 918} Chain breaks: 12 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 4.31, per 1000 atoms: 0.19 Number of scatterers: 22813 At special positions: 0 Unit cell: (126.9, 132.3, 155.25, 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 120 16.00 O 4373 8.00 N 3757 7.00 C 14563 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.05 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.02 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.04 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.06 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.04 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.04 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.05 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=1.99 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.05 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.02 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.04 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.06 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.05 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.04 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.05 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.05 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.02 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.04 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.05 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.04 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.04 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.05 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=1.98 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.04 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 A1301 " - " ASN A 227 " " NAG A1302 " - " ASN A 269 " " NAG A1303 " - " ASN A 699 " " NAG A1304 " - " ASN A 783 " " NAG A1305 " - " ASN A1080 " " NAG B1301 " - " ASN B1080 " " NAG B1302 " - " ASN B 158 " " NAG B1303 " - " ASN B 227 " " NAG B1304 " - " ASN B 318 " " NAG B1305 " - " ASN B 699 " " NAG B1306 " - " ASN B 783 " " NAG C1301 " - " ASN C1080 " " NAG C1302 " - " ASN C 227 " " NAG C1303 " - " ASN C 318 " " NAG C1304 " - " ASN C 699 " " NAG C1305 " - " ASN C 783 " " NAG C1306 " - " ASN C1116 " " NAG C1307 " - " ASN C 269 " Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 1.1 seconds 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5420 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 47 sheets defined 25.2% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 removed outlier: 3.539A pdb=" N GLU A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 removed outlier: 3.763A pdb=" N PHE A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 340 removed outlier: 4.182A pdb=" N TRP A 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 394 through 398 removed outlier: 4.016A pdb=" N ALA A 398 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 603 through 612 Processing helix chain 'A' and resid 719 through 725 Processing helix chain 'A' and resid 729 through 735 Processing helix chain 'A' and resid 736 through 739 removed outlier: 3.618A pdb=" N GLY A 739 " --> pdb=" O LEU A 736 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 736 through 739' Processing helix chain 'A' and resid 741 through 765 Processing helix chain 'A' and resid 798 through 808 removed outlier: 3.637A pdb=" N VAL A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 867 Processing helix chain 'A' and resid 879 through 892 Processing helix chain 'A' and resid 895 through 900 Processing helix chain 'A' and resid 901 through 922 Processing helix chain 'A' and resid 927 through 947 removed outlier: 3.517A pdb=" N GLN A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 967 through 1015 removed outlier: 4.293A pdb=" N VAL A 973 " --> pdb=" O VAL A 969 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 290 removed outlier: 3.656A pdb=" N GLU B 285 " --> pdb=" O ASN B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 336 through 340 removed outlier: 4.118A pdb=" N TRP B 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 376 removed outlier: 4.256A pdb=" N ASN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP B 376 " --> pdb=" O LYS B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 Processing helix chain 'B' and resid 603 through 612 Processing helix chain 'B' and resid 719 through 724 Processing helix chain 'B' and resid 729 through 736 removed outlier: 3.802A pdb=" N ASN B 733 " --> pdb=" O THR B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 739 No H-bonds generated for 'chain 'B' and resid 737 through 739' Processing helix chain 'B' and resid 741 through 765 Processing helix chain 'B' and resid 798 through 808 removed outlier: 3.593A pdb=" N VAL B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 866 Processing helix chain 'B' and resid 879 through 891 Processing helix chain 'B' and resid 895 through 901 removed outlier: 3.736A pdb=" N ASN B 901 " --> pdb=" O VAL B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 922 Processing helix chain 'B' and resid 927 through 947 removed outlier: 3.510A pdb=" N GLN B 931 " --> pdb=" O LEU B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 966 Processing helix chain 'B' and resid 967 through 1015 removed outlier: 4.432A pdb=" N VAL B 973 " --> pdb=" O VAL B 969 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B1015 " --> pdb=" O MET B1011 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 removed outlier: 3.526A pdb=" N GLU C 285 " --> pdb=" O ASN C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 330 removed outlier: 3.976A pdb=" N VAL C 328 " --> pdb=" O PRO C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 340 removed outlier: 4.224A pdb=" N TRP C 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 357 removed outlier: 4.264A pdb=" N TYR C 356 " --> pdb=" O TYR C 352 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN C 357 " --> pdb=" O SER C 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 352 through 357' Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 404 through 409 Processing helix chain 'C' and resid 602 through 612 removed outlier: 4.069A pdb=" N VAL C 606 " --> pdb=" O ASN C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 725 Processing helix chain 'C' and resid 729 through 736 Processing helix chain 'C' and resid 737 through 739 No H-bonds generated for 'chain 'C' and resid 737 through 739' Processing helix chain 'C' and resid 741 through 765 removed outlier: 3.768A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 808 removed outlier: 3.743A pdb=" N VAL C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 867 Processing helix chain 'C' and resid 879 through 891 Processing helix chain 'C' and resid 895 through 901 removed outlier: 3.641A pdb=" N ASN C 901 " --> pdb=" O VAL C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 922 Processing helix chain 'C' and resid 927 through 947 removed outlier: 3.925A pdb=" N GLN C 931 " --> pdb=" O LEU C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 966 removed outlier: 3.521A pdb=" N ILE C 962 " --> pdb=" O VAL C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 1015 removed outlier: 4.146A pdb=" N VAL C 973 " --> pdb=" O VAL C 969 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C1015 " --> pdb=" O MET C1011 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 3.552A pdb=" N HIS A 33 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 187 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N TYR A 200 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N THR A 215 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 47 removed outlier: 6.785A pdb=" N GLY C 552 " --> pdb=" O ASP C 560 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 59 removed outlier: 7.380A pdb=" N THR A 261 " --> pdb=" O ASP A 277 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ASP A 277 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N MET A 263 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ALA A 275 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LYS A 265 " --> pdb=" O THR A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 82 removed outlier: 7.193A pdb=" N ASN A 230 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N PHE A 103 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ARG A 232 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N TRP A 101 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE A 234 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 123 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 165 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE A 161 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 298 through 306 removed outlier: 6.995A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN A 304 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY A 579 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY A 580 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 312 through 315 removed outlier: 3.552A pdb=" N PHE A 527 " --> pdb=" O GLY A 534 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 534 " --> pdb=" O PHE A 527 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLY A 552 " --> pdb=" O ASP A 560 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.530A pdb=" N GLU A 341 " --> pdb=" O SER A 386 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 378 through 379 removed outlier: 3.707A pdb=" N PHE A 379 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AB1, first strand: chain 'A' and resid 640 through 641 Processing sheet with id=AB2, first strand: chain 'A' and resid 683 through 685 removed outlier: 3.558A pdb=" N SER A 685 " --> pdb=" O MET B 770 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 693 through 695 removed outlier: 3.995A pdb=" N THR A1058 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A1060 " --> pdb=" O PHE A1077 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE A1077 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 699 through 710 removed outlier: 3.723A pdb=" N ALA A1038 " --> pdb=" O GLY A1041 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 715 through 718 removed outlier: 4.532A pdb=" N LYS A 715 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 769 through 770 removed outlier: 3.564A pdb=" N MET A 770 " --> pdb=" O ALA C 683 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 778 through 779 removed outlier: 3.591A pdb=" N PHE A 782 " --> pdb=" O PHE A 779 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1102 through 1104 Processing sheet with id=AB9, first strand: chain 'B' and resid 32 through 35 removed outlier: 3.940A pdb=" N SER B 64 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LEU B 194 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LYS B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TYR B 200 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N THR B 215 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL B 40 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 52 through 59 removed outlier: 3.835A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 81 through 82 removed outlier: 4.105A pdb=" N GLY B 100 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS B 128 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN B 122 " --> pdb=" O ASN B 119 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 123 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE B 161 " --> pdb=" O ALA B 127 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 297 through 306 removed outlier: 7.042A pdb=" N VAL B 581 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN B 304 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY B 579 " --> pdb=" O ASN B 304 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 313 through 315 Processing sheet with id=AC5, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.602A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 420 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS B 365 " --> pdb=" O VAL B 420 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 378 through 379 Processing sheet with id=AC7, first strand: chain 'B' and resid 537 through 540 Processing sheet with id=AC8, first strand: chain 'B' and resid 640 through 641 removed outlier: 3.555A pdb=" N SER B 659 " --> pdb=" O VAL B 675 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA B 658 " --> pdb=" O PRO B 651 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 683 through 685 removed outlier: 7.116A pdb=" N ALA B 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 693 through 695 removed outlier: 4.405A pdb=" N THR B1058 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B1060 " --> pdb=" O PHE B1077 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 700 through 710 removed outlier: 3.548A pdb=" N SER B 703 " --> pdb=" O THR B1048 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET B1032 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 715 through 718 removed outlier: 4.548A pdb=" N LYS B 715 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 778 through 779 removed outlier: 3.592A pdb=" N PHE B 782 " --> pdb=" O PHE B 779 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1102 through 1104 Processing sheet with id=AD6, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AD7, first strand: chain 'C' and resid 40 through 41 removed outlier: 7.157A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N THR C 215 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N TYR C 200 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU C 194 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE C 187 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR C 88 " --> pdb=" O GLY C 255 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 52 through 59 removed outlier: 3.941A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 81 through 82 removed outlier: 6.962A pdb=" N ASN C 230 " --> pdb=" O PHE C 103 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N PHE C 103 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG C 232 " --> pdb=" O TRP C 101 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N TRP C 101 " --> pdb=" O ARG C 232 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE C 234 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ARG C 99 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ASN C 118 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP C 101 " --> pdb=" O ILE C 116 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 297 through 306 removed outlier: 6.962A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASN C 304 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLY C 579 " --> pdb=" O ASN C 304 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLY C 580 " --> pdb=" O GLN C 599 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY C 634 " --> pdb=" O THR C 631 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 313 through 315 Processing sheet with id=AE3, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.691A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA C 422 " --> pdb=" O THR C 363 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 378 through 379 Processing sheet with id=AE5, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AE6, first strand: chain 'C' and resid 640 through 641 removed outlier: 3.560A pdb=" N SER C 659 " --> pdb=" O VAL C 675 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 693 through 695 removed outlier: 4.302A pdb=" N THR C1058 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA C1060 " --> pdb=" O PHE C1077 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE C1077 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 700 through 710 removed outlier: 3.743A pdb=" N GLY C1041 " --> pdb=" O ALA C1038 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C1038 " --> pdb=" O GLY C1041 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 715 through 718 removed outlier: 4.571A pdb=" N LYS C 715 " --> pdb=" O LEU C 843 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER C 717 " --> pdb=" O THR C 841 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 778 through 779 Processing sheet with id=AF2, first strand: chain 'C' and resid 1102 through 1107 removed outlier: 5.334A pdb=" N ALA C1069 " --> pdb=" O SER C1105 " (cutoff:3.500A) 937 hydrogen bonds defined for protein. 2589 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: 4.37 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7289 1.34 - 1.48: 6561 1.48 - 1.62: 9286 1.62 - 1.76: 16 1.76 - 1.90: 146 Bond restraints: 23298 Sorted by residual: bond pdb=" C LYS B 411 " pdb=" N LEU B 412 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.07e-02 2.33e+03 1.08e+01 bond pdb=" CB CYS B 720 " pdb=" SG CYS B 720 " ideal model delta sigma weight residual 1.808 1.703 0.105 3.30e-02 9.18e+02 1.01e+01 bond pdb=" CB CYS A 720 " pdb=" SG CYS A 720 " ideal model delta sigma weight residual 1.808 1.708 0.100 3.30e-02 9.18e+02 9.12e+00 bond pdb=" CG LEU B 898 " pdb=" CD1 LEU B 898 " ideal model delta sigma weight residual 1.521 1.428 0.093 3.30e-02 9.18e+02 8.01e+00 bond pdb=" CB CYS B 511 " pdb=" SG CYS B 511 " ideal model delta sigma weight residual 1.808 1.898 -0.090 3.30e-02 9.18e+02 7.46e+00 ... (remaining 23293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.09: 31392 4.09 - 8.18: 213 8.18 - 12.27: 27 12.27 - 16.36: 6 16.36 - 20.45: 1 Bond angle restraints: 31639 Sorted by residual: angle pdb=" CA CYS A 378 " pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " ideal model delta sigma weight residual 114.40 134.85 -20.45 2.30e+00 1.89e-01 7.90e+01 angle pdb=" CA CYS B 378 " pdb=" CB CYS B 378 " pdb=" SG CYS B 378 " ideal model delta sigma weight residual 114.40 130.32 -15.92 2.30e+00 1.89e-01 4.79e+01 angle pdb=" N GLY C1081 " pdb=" CA GLY C1081 " pdb=" C GLY C1081 " ideal model delta sigma weight residual 113.58 106.65 6.93 1.07e+00 8.73e-01 4.19e+01 angle pdb=" CA CYS A 511 " pdb=" CB CYS A 511 " pdb=" SG CYS A 511 " ideal model delta sigma weight residual 114.40 129.07 -14.67 2.30e+00 1.89e-01 4.07e+01 angle pdb=" CA CYS B 419 " pdb=" CB CYS B 419 " pdb=" SG CYS B 419 " ideal model delta sigma weight residual 114.40 128.94 -14.54 2.30e+00 1.89e-01 3.99e+01 ... (remaining 31634 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 12413 18.00 - 36.00: 1105 36.00 - 53.99: 175 53.99 - 71.99: 36 71.99 - 89.99: 20 Dihedral angle restraints: 13749 sinusoidal: 5348 harmonic: 8401 Sorted by residual: dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 511 " pdb=" CB CYS A 511 " ideal model delta sinusoidal sigma weight residual 93.00 11.42 81.58 1 1.00e+01 1.00e-02 8.19e+01 dihedral pdb=" CB CYS A 524 " pdb=" SG CYS A 524 " pdb=" SG CYS A 576 " pdb=" CB CYS A 576 " ideal model delta sinusoidal sigma weight residual -86.00 -16.98 -69.02 1 1.00e+01 1.00e-02 6.16e+01 dihedral pdb=" CA CYS B 603 " pdb=" C CYS B 603 " pdb=" N THR B 604 " pdb=" CA THR B 604 " ideal model delta harmonic sigma weight residual 180.00 143.74 36.26 0 5.00e+00 4.00e-02 5.26e+01 ... (remaining 13746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 3596 0.160 - 0.321: 57 0.321 - 0.481: 5 0.481 - 0.641: 0 0.641 - 0.801: 1 Chirality restraints: 3659 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 227 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" CB VAL C 606 " pdb=" CA VAL C 606 " pdb=" CG1 VAL C 606 " pdb=" CG2 VAL C 606 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" CG LEU C 898 " pdb=" CB LEU C 898 " pdb=" CD1 LEU C 898 " pdb=" CD2 LEU C 898 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.88e+00 ... (remaining 3656 not shown) Planarity restraints: 4066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 227 " 0.003 2.00e-02 2.50e+03 3.42e-02 1.46e+01 pdb=" CG ASN C 227 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN C 227 " 0.040 2.00e-02 2.50e+03 pdb=" ND2 ASN C 227 " -0.040 2.00e-02 2.50e+03 pdb=" C1 NAG C1302 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 323 " 0.063 5.00e-02 4.00e+02 9.24e-02 1.37e+01 pdb=" N PRO A 324 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO A 324 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 324 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 158 " 0.029 2.00e-02 2.50e+03 2.90e-02 1.05e+01 pdb=" CG ASN B 158 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN B 158 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B 158 " -0.042 2.00e-02 2.50e+03 pdb=" C1 NAG B1302 " 0.035 2.00e-02 2.50e+03 ... (remaining 4063 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1526 2.73 - 3.27: 19718 3.27 - 3.81: 33566 3.81 - 4.36: 41903 4.36 - 4.90: 76858 Nonbonded interactions: 173571 Sorted by model distance: nonbonded pdb=" O SER A 380 " pdb=" OG1 THR A 509 " model vdw 2.182 3.040 nonbonded pdb=" O SER B 380 " pdb=" OG1 THR B 509 " model vdw 2.191 3.040 nonbonded pdb=" O SER A 35 " pdb=" OG SER A 35 " model vdw 2.252 3.040 nonbonded pdb=" OG1 THR A1098 " pdb=" OD1 ASP A1100 " model vdw 2.254 3.040 nonbonded pdb=" OG1 THR A 698 " pdb=" O GLN A1053 " model vdw 2.254 3.040 ... (remaining 173566 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 31 through 131 or resid 155 through 235 or resid 250 throu \ gh 425 or resid 439 through 455 or resid 492 through 810 or resid 818 through 82 \ 3 or resid 832 through 1305)) selection = (chain 'B' and (resid 31 through 131 or resid 155 through 166 or resid 181 throu \ gh 810 or resid 818 through 1305)) selection = (chain 'C' and (resid 31 through 235 or resid 250 through 425 or resid 439 throu \ gh 455 or resid 492 through 1305)) } 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=0.00 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.200 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 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 : 0.011 0.123 23355 Z= 0.446 Angle : 1.081 20.448 31771 Z= 0.566 Chirality : 0.068 0.801 3659 Planarity : 0.007 0.092 4048 Dihedral : 14.039 89.990 8212 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.14), residues: 2812 helix: -0.33 (0.19), residues: 658 sheet: -0.08 (0.20), residues: 661 loop : -2.19 (0.13), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 544 TYR 0.036 0.003 TYR B 200 PHE 0.038 0.004 PHE C 527 TRP 0.015 0.003 TRP C 868 HIS 0.010 0.002 HIS C1046 Details of bonding type rmsd/Z covalent geometry : bond 0.01132 / 0.45 (23298) covalent geometry : angle 1.03336 / 0.55 (31639) SS BOND : bond 0.01575 / 1.17 ( 39) SS BOND : angle 4.05180 / 2.62 ( 78) hydrogen bonds : bond 0.22670 / 14.94 ( 937) hydrogen bonds : angle 7.83859 / 5.37 ( 2589) link_NAG-ASN : bond 0.00617 / 0.39 ( 18) link_NAG-ASN : angle 6.13863 / 3.95 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.743 Fit side-chains REVERT: A 183 ARG cc_start: 0.7370 (ptp-110) cc_final: 0.7168 (mtp180) REVERT: A 1032 MET cc_start: 0.8811 (ptm) cc_final: 0.8510 (ptm) REVERT: B 99 ARG cc_start: 0.6339 (ptt180) cc_final: 0.6139 (mtp85) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.1523 time to fit residues: 60.6709 Evaluate side-chains 222 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 599 GLN B 108 ASN B 835 GLN C1107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.149319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.121969 restraints weight = 24920.643| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.99 r_work: 0.2929 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23355 Z= 0.135 Angle : 0.622 13.075 31771 Z= 0.321 Chirality : 0.046 0.340 3659 Planarity : 0.005 0.056 4048 Dihedral : 5.078 33.051 3080 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.48 % Allowed : 6.11 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.15), residues: 2812 helix: 1.05 (0.20), residues: 668 sheet: 0.44 (0.20), residues: 680 loop : -1.91 (0.14), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 544 TYR 0.016 0.001 TYR A 200 PHE 0.017 0.001 PHE B 387 TRP 0.009 0.001 TRP B 101 HIS 0.003 0.001 HIS C1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (23298) covalent geometry : angle 0.58791 / 0.31 (31639) SS BOND : bond 0.00764 / 0.51 ( 39) SS BOND : angle 2.39401 / 1.48 ( 78) hydrogen bonds : bond 0.07033 / 4.50 ( 937) hydrogen bonds : angle 5.47736 / 3.79 ( 2589) link_NAG-ASN : bond 0.00522 / 0.33 ( 18) link_NAG-ASN : angle 4.07667 / 2.62 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 234 time to evaluate : 0.675 Fit side-chains REVERT: A 130 PHE cc_start: 0.8636 (m-80) cc_final: 0.8356 (m-80) REVERT: A 352 TYR cc_start: 0.8567 (m-80) cc_final: 0.7441 (m-80) REVERT: A 1032 MET cc_start: 0.9230 (ptm) cc_final: 0.9014 (ptm) REVERT: A 1074 GLU cc_start: 0.8149 (pt0) cc_final: 0.7809 (pt0) REVERT: B 99 ARG cc_start: 0.6537 (ptt180) cc_final: 0.5327 (ptp-110) REVERT: B 405 ILE cc_start: 0.7484 (mt) cc_final: 0.7259 (mt) REVERT: B 882 MET cc_start: 0.9011 (mtt) cc_final: 0.8764 (mtm) REVERT: C 111 SER cc_start: 0.8228 (m) cc_final: 0.8019 (m) REVERT: C 160 THR cc_start: 0.7802 (p) cc_final: 0.6972 (t) REVERT: C 550 GLN cc_start: 0.7942 (tp40) cc_final: 0.7558 (tp40) outliers start: 12 outliers final: 6 residues processed: 241 average time/residue: 0.1341 time to fit residues: 51.9536 Evaluate side-chains 220 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 214 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 679 MET Chi-restraints excluded: chain C residue 691 ASN Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 116 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 81 optimal weight: 0.0370 chunk 239 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 213 optimal weight: 0.1980 chunk 61 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 HIS A 786 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.165815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.158484 restraints weight = 24195.682| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 0.48 r_work: 0.3281 rms_B_bonded: 0.88 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 1.87 restraints_weight: 0.2500 r_work: 0.3010 rms_B_bonded: 3.39 restraints_weight: 0.1250 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 23355 Z= 0.109 Angle : 0.544 11.198 31771 Z= 0.280 Chirality : 0.044 0.297 3659 Planarity : 0.004 0.045 4048 Dihedral : 4.453 29.320 3080 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.32 % Allowed : 7.98 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.15), residues: 2812 helix: 1.88 (0.21), residues: 655 sheet: 0.58 (0.20), residues: 672 loop : -1.76 (0.14), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 544 TYR 0.016 0.001 TYR C1049 PHE 0.014 0.001 PHE C 364 TRP 0.008 0.001 TRP C 868 HIS 0.002 0.000 HIS C1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (23298) covalent geometry : angle 0.51428 / 0.27 (31639) SS BOND : bond 0.00523 / 0.36 ( 39) SS BOND : angle 2.15245 / 1.32 ( 78) hydrogen bonds : bond 0.05628 / 3.59 ( 937) hydrogen bonds : angle 4.88107 / 3.39 ( 2589) link_NAG-ASN : bond 0.00523 / 0.34 ( 18) link_NAG-ASN : angle 3.55736 / 2.27 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 230 time to evaluate : 0.638 Fit side-chains REVERT: A 130 PHE cc_start: 0.8722 (m-80) cc_final: 0.8520 (m-80) REVERT: A 183 ARG cc_start: 0.8003 (ptp-170) cc_final: 0.7752 (mtt180) REVERT: A 352 TYR cc_start: 0.8455 (m-80) cc_final: 0.7454 (m-80) REVERT: A 1032 MET cc_start: 0.9026 (ptm) cc_final: 0.8796 (ptm) REVERT: A 1074 GLU cc_start: 0.7917 (pt0) cc_final: 0.7578 (pt0) REVERT: B 99 ARG cc_start: 0.6602 (ptt180) cc_final: 0.5650 (ptp-110) REVERT: B 405 ILE cc_start: 0.7430 (mt) cc_final: 0.7144 (mt) REVERT: B 796 LYS cc_start: 0.7937 (ttmt) cc_final: 0.7518 (mmtm) REVERT: B 882 MET cc_start: 0.9053 (mtt) cc_final: 0.8842 (mtm) REVERT: C 110 LYS cc_start: 0.8516 (ptpp) cc_final: 0.7611 (tptt) REVERT: C 160 THR cc_start: 0.7175 (p) cc_final: 0.6602 (t) REVERT: C 183 ARG cc_start: 0.7714 (mtt180) cc_final: 0.7133 (mtt-85) outliers start: 33 outliers final: 19 residues processed: 252 average time/residue: 0.1375 time to fit residues: 56.1143 Evaluate side-chains 230 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 211 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 848 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 13 optimal weight: 0.6980 chunk 174 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 272 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 176 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.148073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.121333 restraints weight = 24916.569| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.77 r_work: 0.2922 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 23355 Z= 0.170 Angle : 0.611 13.263 31771 Z= 0.312 Chirality : 0.047 0.276 3659 Planarity : 0.004 0.044 4048 Dihedral : 4.636 32.726 3080 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.56 % Allowed : 9.22 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.15), residues: 2812 helix: 1.81 (0.21), residues: 649 sheet: 0.70 (0.21), residues: 673 loop : -1.80 (0.14), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 544 TYR 0.018 0.001 TYR C1049 PHE 0.021 0.002 PHE A 83 TRP 0.009 0.001 TRP C 868 HIS 0.004 0.001 HIS C1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 (23298) covalent geometry : angle 0.57972 / 0.30 (31639) SS BOND : bond 0.00772 / 0.54 ( 39) SS BOND : angle 2.54419 / 1.57 ( 78) hydrogen bonds : bond 0.06983 / 4.43 ( 937) hydrogen bonds : angle 4.95908 / 3.43 ( 2589) link_NAG-ASN : bond 0.00490 / 0.32 ( 18) link_NAG-ASN : angle 3.66565 / 2.35 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 221 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 PHE cc_start: 0.8705 (m-80) cc_final: 0.8439 (m-80) REVERT: A 352 TYR cc_start: 0.8500 (m-80) cc_final: 0.7504 (m-80) REVERT: A 1032 MET cc_start: 0.9148 (ptm) cc_final: 0.8890 (ptm) REVERT: A 1074 GLU cc_start: 0.7951 (pt0) cc_final: 0.7577 (pt0) REVERT: B 99 ARG cc_start: 0.6508 (ptt180) cc_final: 0.5430 (ptp-110) REVERT: B 396 GLN cc_start: 0.8417 (tt0) cc_final: 0.8170 (tt0) REVERT: B 796 LYS cc_start: 0.7884 (ttmt) cc_final: 0.7376 (mmtm) REVERT: B 959 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8302 (mp) REVERT: C 110 LYS cc_start: 0.8475 (ptpp) cc_final: 0.7320 (tptt) REVERT: C 160 THR cc_start: 0.7272 (p) cc_final: 0.6647 (t) outliers start: 39 outliers final: 33 residues processed: 248 average time/residue: 0.1347 time to fit residues: 53.4197 Evaluate side-chains 248 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 214 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 544 ARG Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 915 GLN Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 146 optimal weight: 4.9990 chunk 175 optimal weight: 0.0570 chunk 185 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 221 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 129 optimal weight: 0.0270 chunk 17 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 chunk 275 optimal weight: 0.6980 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN A 281 ASN B 108 ASN B 746 ASN C 108 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.150978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.126634 restraints weight = 24582.918| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.11 r_work: 0.3013 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 23355 Z= 0.103 Angle : 0.524 10.699 31771 Z= 0.269 Chirality : 0.044 0.286 3659 Planarity : 0.004 0.040 4048 Dihedral : 4.243 29.105 3080 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.60 % Allowed : 10.34 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.16), residues: 2812 helix: 2.25 (0.21), residues: 650 sheet: 0.75 (0.21), residues: 665 loop : -1.67 (0.14), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 544 TYR 0.015 0.001 TYR C1049 PHE 0.012 0.001 PHE C1103 TRP 0.009 0.001 TRP C 868 HIS 0.001 0.000 HIS A1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (23298) covalent geometry : angle 0.49538 / 0.26 (31639) SS BOND : bond 0.00566 / 0.39 ( 39) SS BOND : angle 2.05497 / 1.26 ( 78) hydrogen bonds : bond 0.05349 / 3.41 ( 937) hydrogen bonds : angle 4.67450 / 3.24 ( 2589) link_NAG-ASN : bond 0.00506 / 0.33 ( 18) link_NAG-ASN : angle 3.38644 / 2.17 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 226 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 130 PHE cc_start: 0.8606 (m-80) cc_final: 0.8392 (m-80) REVERT: A 183 ARG cc_start: 0.8037 (ptp-170) cc_final: 0.7820 (mtt180) REVERT: A 352 TYR cc_start: 0.8515 (m-80) cc_final: 0.7623 (m-80) REVERT: A 898 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8125 (tp) REVERT: A 1032 MET cc_start: 0.9034 (ptm) cc_final: 0.8830 (ptm) REVERT: A 1074 GLU cc_start: 0.7949 (pt0) cc_final: 0.7654 (pt0) REVERT: B 99 ARG cc_start: 0.6767 (ptt180) cc_final: 0.5807 (ptp-110) REVERT: B 796 LYS cc_start: 0.7933 (ttmt) cc_final: 0.7521 (mmtm) REVERT: C 110 LYS cc_start: 0.8395 (ptpp) cc_final: 0.7412 (tptt) REVERT: C 903 LYS cc_start: 0.8112 (mppt) cc_final: 0.7531 (mmmt) outliers start: 40 outliers final: 31 residues processed: 253 average time/residue: 0.1329 time to fit residues: 54.0998 Evaluate side-chains 245 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 213 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 544 ARG Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 915 GLN Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 70 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 134 optimal weight: 0.7980 chunk 276 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 113 optimal weight: 0.0030 chunk 171 optimal weight: 0.6980 chunk 234 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN B 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.150840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.135523 restraints weight = 24804.175| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 0.81 r_work: 0.3199 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 23355 Z= 0.109 Angle : 0.529 14.519 31771 Z= 0.271 Chirality : 0.044 0.277 3659 Planarity : 0.004 0.041 4048 Dihedral : 4.173 27.784 3080 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.72 % Allowed : 10.42 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.16), residues: 2812 helix: 2.38 (0.21), residues: 650 sheet: 0.82 (0.21), residues: 665 loop : -1.61 (0.14), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 544 TYR 0.016 0.001 TYR C1049 PHE 0.014 0.001 PHE A 83 TRP 0.010 0.001 TRP C 868 HIS 0.002 0.000 HIS C1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (23298) covalent geometry : angle 0.50240 / 0.26 (31639) SS BOND : bond 0.00591 / 0.40 ( 39) SS BOND : angle 2.05643 / 1.26 ( 78) hydrogen bonds : bond 0.05479 / 3.49 ( 937) hydrogen bonds : angle 4.61602 / 3.19 ( 2589) link_NAG-ASN : bond 0.00506 / 0.33 ( 18) link_NAG-ASN : angle 3.29488 / 2.10 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 225 time to evaluate : 0.833 Fit side-chains REVERT: A 56 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8301 (tp40) REVERT: A 183 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7676 (mtt180) REVERT: A 352 TYR cc_start: 0.8430 (m-80) cc_final: 0.7561 (m-80) REVERT: A 987 GLN cc_start: 0.8256 (mm-40) cc_final: 0.7604 (mm-40) REVERT: A 1074 GLU cc_start: 0.7816 (pt0) cc_final: 0.7517 (pt0) REVERT: B 99 ARG cc_start: 0.6697 (ptt180) cc_final: 0.5879 (ptp-110) REVERT: B 796 LYS cc_start: 0.7932 (ttmt) cc_final: 0.7685 (mmtm) REVERT: C 110 LYS cc_start: 0.8318 (ptpp) cc_final: 0.7626 (tptt) REVERT: C 903 LYS cc_start: 0.7986 (mppt) cc_final: 0.7493 (mmmt) outliers start: 43 outliers final: 35 residues processed: 254 average time/residue: 0.1397 time to fit residues: 56.9201 Evaluate side-chains 248 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 211 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 544 ARG Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 915 GLN Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 241 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 255 optimal weight: 4.9990 chunk 264 optimal weight: 0.0970 chunk 246 optimal weight: 0.6980 chunk 200 optimal weight: 0.0770 chunk 138 optimal weight: 1.9990 chunk 270 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 133 optimal weight: 0.3980 chunk 261 optimal weight: 0.6980 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN B 108 ASN B 357 ASN B 505 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.152844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.128139 restraints weight = 24710.453| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.32 r_work: 0.3010 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 23355 Z= 0.096 Angle : 0.501 13.892 31771 Z= 0.257 Chirality : 0.043 0.281 3659 Planarity : 0.003 0.042 4048 Dihedral : 3.977 26.133 3080 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.76 % Allowed : 11.05 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.16), residues: 2812 helix: 2.68 (0.21), residues: 641 sheet: 0.89 (0.20), residues: 670 loop : -1.51 (0.15), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 544 TYR 0.016 0.001 TYR C1049 PHE 0.013 0.001 PHE C1103 TRP 0.009 0.001 TRP C 868 HIS 0.002 0.000 HIS C1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 (23298) covalent geometry : angle 0.47614 / 0.25 (31639) SS BOND : bond 0.00571 / 0.36 ( 39) SS BOND : angle 1.86120 / 1.15 ( 78) hydrogen bonds : bond 0.04868 / 3.11 ( 937) hydrogen bonds : angle 4.48524 / 3.10 ( 2589) link_NAG-ASN : bond 0.00512 / 0.33 ( 18) link_NAG-ASN : angle 3.15926 / 2.01 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 228 time to evaluate : 0.647 Fit side-chains REVERT: A 56 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8377 (tp40) REVERT: A 129 ASN cc_start: 0.7104 (m110) cc_final: 0.6699 (m110) REVERT: A 352 TYR cc_start: 0.8467 (m-80) cc_final: 0.7530 (m-80) REVERT: A 987 GLN cc_start: 0.8331 (mm-40) cc_final: 0.7763 (mm-40) REVERT: B 99 ARG cc_start: 0.6555 (ptt180) cc_final: 0.5527 (ptp-110) REVERT: B 796 LYS cc_start: 0.7917 (ttmt) cc_final: 0.7476 (mmtm) REVERT: C 110 LYS cc_start: 0.8468 (ptpp) cc_final: 0.7370 (tptt) REVERT: C 352 TYR cc_start: 0.8049 (m-80) cc_final: 0.7687 (m-80) REVERT: C 589 ASN cc_start: 0.7835 (p0) cc_final: 0.7372 (t0) REVERT: C 903 LYS cc_start: 0.7918 (mppt) cc_final: 0.7267 (mmmt) outliers start: 44 outliers final: 35 residues processed: 260 average time/residue: 0.1256 time to fit residues: 53.0641 Evaluate side-chains 255 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 219 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 1025 CYS Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 544 ARG Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 122 optimal weight: 5.9990 chunk 254 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 217 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN B 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.147546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.133438 restraints weight = 24708.048| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 0.76 r_work: 0.3190 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 23355 Z= 0.171 Angle : 0.596 13.799 31771 Z= 0.305 Chirality : 0.047 0.269 3659 Planarity : 0.004 0.045 4048 Dihedral : 4.371 28.450 3080 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.80 % Allowed : 11.29 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.16), residues: 2812 helix: 2.24 (0.21), residues: 637 sheet: 0.94 (0.21), residues: 654 loop : -1.62 (0.14), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 544 TYR 0.018 0.001 TYR C1049 PHE 0.020 0.002 PHE A 83 TRP 0.006 0.001 TRP B 868 HIS 0.003 0.001 HIS A1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.17 (23298) covalent geometry : angle 0.56830 / 0.30 (31639) SS BOND : bond 0.00730 / 0.51 ( 39) SS BOND : angle 2.37977 / 1.48 ( 78) hydrogen bonds : bond 0.06896 / 4.37 ( 937) hydrogen bonds : angle 4.77833 / 3.30 ( 2589) link_NAG-ASN : bond 0.00470 / 0.30 ( 18) link_NAG-ASN : angle 3.43270 / 2.20 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 215 time to evaluate : 0.781 Fit side-chains REVERT: A 56 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8240 (tp40) REVERT: A 352 TYR cc_start: 0.8366 (m-80) cc_final: 0.7520 (m-80) REVERT: A 987 GLN cc_start: 0.8294 (mm-40) cc_final: 0.7696 (mm-40) REVERT: B 99 ARG cc_start: 0.6638 (ptt180) cc_final: 0.5937 (ptp-110) REVERT: B 796 LYS cc_start: 0.7846 (ttmt) cc_final: 0.7637 (mmtm) REVERT: C 110 LYS cc_start: 0.8276 (ptpp) cc_final: 0.7760 (tptt) REVERT: C 352 TYR cc_start: 0.8063 (m-80) cc_final: 0.7797 (m-80) REVERT: C 1068 LYS cc_start: 0.8336 (pttm) cc_final: 0.8084 (mtmt) outliers start: 45 outliers final: 40 residues processed: 249 average time/residue: 0.1306 time to fit residues: 53.0009 Evaluate side-chains 246 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 205 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 1025 CYS Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 544 ARG Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 43 optimal weight: 5.9990 chunk 179 optimal weight: 0.9990 chunk 255 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 245 optimal weight: 3.9990 chunk 212 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN B 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.146605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.122501 restraints weight = 24955.966| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.97 r_work: 0.3022 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 23355 Z= 0.190 Angle : 0.636 13.700 31771 Z= 0.325 Chirality : 0.048 0.268 3659 Planarity : 0.004 0.045 4048 Dihedral : 4.620 30.968 3080 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.80 % Allowed : 11.77 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.16), residues: 2812 helix: 1.89 (0.20), residues: 641 sheet: 0.81 (0.21), residues: 641 loop : -1.68 (0.14), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 544 TYR 0.018 0.001 TYR C1049 PHE 0.021 0.002 PHE A 83 TRP 0.007 0.001 TRP B 868 HIS 0.005 0.001 HIS C1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.19 (23298) covalent geometry : angle 0.60616 / 0.32 (31639) SS BOND : bond 0.00784 / 0.56 ( 39) SS BOND : angle 2.58443 / 1.60 ( 78) hydrogen bonds : bond 0.07395 / 4.69 ( 937) hydrogen bonds : angle 4.90297 / 3.39 ( 2589) link_NAG-ASN : bond 0.00469 / 0.30 ( 18) link_NAG-ASN : angle 3.61237 / 2.32 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 216 time to evaluate : 0.678 Fit side-chains REVERT: A 56 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8349 (tp40) REVERT: A 352 TYR cc_start: 0.8511 (m-80) cc_final: 0.7646 (m-80) REVERT: B 99 ARG cc_start: 0.6831 (ptt180) cc_final: 0.6054 (ptp-110) REVERT: B 796 LYS cc_start: 0.7939 (ttmt) cc_final: 0.7626 (mmtm) REVERT: C 110 LYS cc_start: 0.8490 (ptpp) cc_final: 0.7847 (tptt) REVERT: C 352 TYR cc_start: 0.8184 (m-80) cc_final: 0.7847 (m-80) REVERT: C 1068 LYS cc_start: 0.8446 (pttm) cc_final: 0.8106 (mtmt) outliers start: 45 outliers final: 38 residues processed: 249 average time/residue: 0.1341 time to fit residues: 53.3460 Evaluate side-chains 250 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 211 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 1025 CYS Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 544 ARG Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 226 optimal weight: 8.9990 chunk 130 optimal weight: 0.4980 chunk 194 optimal weight: 1.9990 chunk 270 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 264 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 202 optimal weight: 0.0970 chunk 36 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN B 108 ASN B 937 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.147430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.132390 restraints weight = 24922.642| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 0.80 r_work: 0.3221 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 23355 Z= 0.157 Angle : 0.597 13.428 31771 Z= 0.305 Chirality : 0.046 0.271 3659 Planarity : 0.004 0.044 4048 Dihedral : 4.511 33.834 3080 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.72 % Allowed : 11.97 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.16), residues: 2812 helix: 1.99 (0.21), residues: 643 sheet: 0.91 (0.21), residues: 661 loop : -1.70 (0.14), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 544 TYR 0.017 0.001 TYR C1049 PHE 0.018 0.002 PHE A 83 TRP 0.008 0.001 TRP C 868 HIS 0.004 0.001 HIS C1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (23298) covalent geometry : angle 0.56759 / 0.30 (31639) SS BOND : bond 0.00712 / 0.50 ( 39) SS BOND : angle 2.40345 / 1.49 ( 78) hydrogen bonds : bond 0.06743 / 4.29 ( 937) hydrogen bonds : angle 4.81337 / 3.32 ( 2589) link_NAG-ASN : bond 0.00471 / 0.31 ( 18) link_NAG-ASN : angle 3.50935 / 2.25 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5624 Ramachandran restraints generated. 2812 Oldfield, 0 Emsley, 2812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 209 time to evaluate : 0.885 Fit side-chains REVERT: A 56 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8213 (tp40) REVERT: A 352 TYR cc_start: 0.8312 (m-80) cc_final: 0.7489 (m-80) REVERT: A 987 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7719 (mm-40) REVERT: B 99 ARG cc_start: 0.6722 (ptt180) cc_final: 0.6098 (ptp-110) REVERT: B 796 LYS cc_start: 0.7872 (ttmt) cc_final: 0.7650 (mmtm) REVERT: C 110 LYS cc_start: 0.8315 (ptpp) cc_final: 0.7915 (tptt) REVERT: C 1068 LYS cc_start: 0.8331 (pttm) cc_final: 0.8020 (mtmt) outliers start: 43 outliers final: 40 residues processed: 240 average time/residue: 0.1411 time to fit residues: 54.2593 Evaluate side-chains 249 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 208 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 511 CYS Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 848 THR Chi-restraints excluded: chain A residue 914 SER Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 1025 CYS Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 544 ARG Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 1082 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 71 optimal weight: 2.9990 chunk 206 optimal weight: 0.8980 chunk 266 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 279 optimal weight: 2.9990 chunk 274 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 72 optimal weight: 0.0970 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN B 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.150059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.136055 restraints weight = 24787.370| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 0.76 r_work: 0.3205 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 23355 Z= 0.116 Angle : 0.544 13.093 31771 Z= 0.278 Chirality : 0.045 0.277 3659 Planarity : 0.004 0.043 4048 Dihedral : 4.233 30.894 3080 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.60 % Allowed : 12.29 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.16), residues: 2812 helix: 2.31 (0.21), residues: 645 sheet: 0.87 (0.21), residues: 663 loop : -1.59 (0.14), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 544 TYR 0.016 0.001 TYR C1049 PHE 0.014 0.001 PHE A 83 TRP 0.007 0.001 TRP C 868 HIS 0.003 0.000 HIS C1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (23298) covalent geometry : angle 0.51767 / 0.27 (31639) SS BOND : bond 0.00599 / 0.41 ( 39) SS BOND : angle 2.07532 / 1.28 ( 78) hydrogen bonds : bond 0.05643 / 3.60 ( 937) hydrogen bonds : angle 4.62100 / 3.19 ( 2589) link_NAG-ASN : bond 0.00502 / 0.33 ( 18) link_NAG-ASN : angle 3.27425 / 2.09 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4618.24 seconds wall clock time: 79 minutes 49.48 seconds (4789.48 seconds total)