Starting phenix.real_space_refine on Thu Jun 19 19:01:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h15_34425/06_2025/8h15_34425.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h15_34425/06_2025/8h15_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_34425/06_2025/8h15_34425.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h15_34425/06_2025/8h15_34425.map" model { file = "/net/cci-nas-00/data/ceres_data/8h15_34425/06_2025/8h15_34425.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h15_34425/06_2025/8h15_34425.cif" } resolution = 3.14182 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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 dihedrals: 15 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 dihedrals: 18 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 dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 13.29, per 1000 atoms: 0.58 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: 5.74 Conformation dependent library (CDL) restraints added in 3.1 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: 3.61 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: 10.71 Time building geometry restraints manager: 6.70 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: 12744 18.00 - 36.00: 1132 36.00 - 53.99: 192 53.99 - 71.99: 39 71.99 - 89.99: 20 Dihedral angle restraints: 14127 sinusoidal: 5726 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 14124 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 1121 or resid 1301 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 1121 or resid 1301 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 1121 or resid 1301 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 55.310 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 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 : 14.032 89.990 8590 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (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 TRP 0.015 0.003 TRP C 868 HIS 0.010 0.002 HIS C1046 PHE 0.038 0.004 PHE C 527 TYR 0.036 0.003 TYR B 200 ARG 0.016 0.001 ARG B 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00617 ( 18) link_NAG-ASN : angle 6.13863 ( 54) hydrogen bonds : bond 0.22670 ( 937) hydrogen bonds : angle 7.83859 ( 2589) SS BOND : bond 0.01575 ( 39) SS BOND : angle 4.05180 ( 78) covalent geometry : bond 0.01132 (23298) covalent geometry : angle 1.03336 (31639) *********************** 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 : 2.420 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: 0.3465 time to fit residues: 138.1017 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 : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 242 optimal weight: 0.9990 chunk 217 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 146 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 224 optimal weight: 9.9990 chunk 87 optimal weight: 0.4980 chunk 136 optimal weight: 0.9980 chunk 167 optimal weight: 0.7980 chunk 260 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3585 r_free = 0.3585 target = 0.150386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.122900 restraints weight = 24707.931| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.91 r_work: 0.2937 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23355 Z= 0.128 Angle : 0.608 12.955 31771 Z= 0.314 Chirality : 0.046 0.347 3659 Planarity : 0.005 0.055 4048 Dihedral : 6.093 59.780 3458 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.56 % Allowed : 6.26 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.15), residues: 2812 helix: 1.13 (0.20), residues: 668 sheet: 0.41 (0.20), residues: 668 loop : -1.90 (0.14), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 101 HIS 0.003 0.001 HIS C1046 PHE 0.016 0.001 PHE B 387 TYR 0.016 0.001 TYR A 200 ARG 0.005 0.000 ARG B 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00519 ( 18) link_NAG-ASN : angle 4.08073 ( 54) hydrogen bonds : bond 0.06592 ( 937) hydrogen bonds : angle 5.37747 ( 2589) SS BOND : bond 0.00604 ( 39) SS BOND : angle 2.30054 ( 78) covalent geometry : bond 0.00280 (23298) covalent geometry : angle 0.57412 (31639) *********************** 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 248 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 234 time to evaluate : 2.601 Fit side-chains REVERT: A 130 PHE cc_start: 0.8748 (m-80) cc_final: 0.8509 (m-80) REVERT: A 183 ARG cc_start: 0.7659 (ptp-110) cc_final: 0.7451 (ptp-170) REVERT: A 352 TYR cc_start: 0.8462 (m-80) cc_final: 0.7323 (m-80) REVERT: A 1032 MET cc_start: 0.9117 (ptm) cc_final: 0.8878 (ptm) REVERT: A 1074 GLU cc_start: 0.7914 (pt0) cc_final: 0.7558 (pt0) REVERT: B 99 ARG cc_start: 0.6483 (ptt180) cc_final: 0.5400 (ptp-110) REVERT: B 405 ILE cc_start: 0.7516 (mt) cc_final: 0.7285 (mt) REVERT: B 882 MET cc_start: 0.8911 (mtt) cc_final: 0.8678 (mtm) REVERT: C 160 THR cc_start: 0.7719 (p) cc_final: 0.6949 (t) REVERT: C 550 GLN cc_start: 0.7750 (tp40) cc_final: 0.7433 (tp40) outliers start: 14 outliers final: 8 residues processed: 244 average time/residue: 0.3342 time to fit residues: 129.8547 Evaluate side-chains 218 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 210 time to evaluate : 2.377 ------------------------------------------------------------------------------- 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 353 SER Chi-restraints excluded: chain C residue 389 VAL 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 139 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 157 optimal weight: 0.0670 chunk 48 optimal weight: 3.9990 chunk 152 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 786 GLN B 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.149289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.132113 restraints weight = 24631.656| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 0.88 r_work: 0.3345 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 23355 Z= 0.133 Angle : 0.582 11.463 31771 Z= 0.299 Chirality : 0.045 0.278 3659 Planarity : 0.004 0.046 4048 Dihedral : 5.628 59.526 3458 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.28 % Allowed : 7.94 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.15), residues: 2812 helix: 1.69 (0.21), residues: 656 sheet: 0.58 (0.20), residues: 682 loop : -1.82 (0.14), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 868 HIS 0.002 0.001 HIS C1046 PHE 0.017 0.001 PHE A 83 TYR 0.017 0.001 TYR C1049 ARG 0.005 0.000 ARG B 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00486 ( 18) link_NAG-ASN : angle 3.80822 ( 54) hydrogen bonds : bond 0.06453 ( 937) hydrogen bonds : angle 5.02635 ( 2589) SS BOND : bond 0.00660 ( 39) SS BOND : angle 2.37094 ( 78) covalent geometry : bond 0.00308 (23298) covalent geometry : angle 0.54915 (31639) *********************** 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 254 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 222 time to evaluate : 2.403 Fit side-chains REVERT: A 352 TYR cc_start: 0.8466 (m-80) cc_final: 0.7517 (m-80) REVERT: A 1032 MET cc_start: 0.8916 (ptm) cc_final: 0.8658 (ptm) REVERT: A 1074 GLU cc_start: 0.7690 (pt0) cc_final: 0.7372 (pt0) REVERT: B 99 ARG cc_start: 0.6706 (ptt180) cc_final: 0.6038 (ptp-110) REVERT: B 364 PHE cc_start: 0.8402 (t80) cc_final: 0.8193 (t80) REVERT: B 405 ILE cc_start: 0.7488 (mt) cc_final: 0.7220 (mt) REVERT: B 882 MET cc_start: 0.8940 (mtt) cc_final: 0.8711 (mtm) REVERT: C 99 ARG cc_start: 0.7610 (ptp-170) cc_final: 0.7328 (ptp90) REVERT: C 110 LYS cc_start: 0.8208 (ptpp) cc_final: 0.7946 (tptt) REVERT: C 160 THR cc_start: 0.7365 (p) cc_final: 0.6788 (t) REVERT: C 183 ARG cc_start: 0.7452 (mtt180) cc_final: 0.7185 (mtt-85) outliers start: 32 outliers final: 21 residues processed: 244 average time/residue: 0.3319 time to fit residues: 128.6352 Evaluate side-chains 226 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 2.363 ------------------------------------------------------------------------------- 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 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 B residue 537 VAL 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 389 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 1109 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 262 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 123 optimal weight: 0.4980 chunk 133 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 278 optimal weight: 3.9990 chunk 239 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.163101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.156343 restraints weight = 24299.866| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 0.44 r_work: 0.3568 rms_B_bonded: 0.85 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 1.58 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 23355 Z= 0.141 Angle : 0.584 12.883 31771 Z= 0.299 Chirality : 0.046 0.264 3659 Planarity : 0.004 0.043 4048 Dihedral : 5.527 58.902 3458 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.16), residues: 2812 helix: 1.86 (0.21), residues: 649 sheet: 0.67 (0.21), residues: 671 loop : -1.80 (0.14), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 868 HIS 0.003 0.001 HIS C1046 PHE 0.017 0.001 PHE A 83 TYR 0.017 0.001 TYR C1049 ARG 0.005 0.000 ARG B 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00476 ( 18) link_NAG-ASN : angle 3.68107 ( 54) hydrogen bonds : bond 0.06510 ( 937) hydrogen bonds : angle 4.92583 ( 2589) SS BOND : bond 0.00731 ( 39) SS BOND : angle 2.39395 ( 78) covalent geometry : bond 0.00336 (23298) covalent geometry : angle 0.55202 (31639) *********************** 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 : 2.574 Fit side-chains revert: symmetry clash REVERT: A 352 TYR cc_start: 0.8182 (m-80) cc_final: 0.7376 (m-80) REVERT: A 1032 MET cc_start: 0.8847 (ptm) cc_final: 0.8585 (ptm) REVERT: A 1074 GLU cc_start: 0.7297 (pt0) cc_final: 0.7014 (pt0) REVERT: B 99 ARG cc_start: 0.6492 (ptt180) cc_final: 0.6090 (ptp-110) REVERT: B 959 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8371 (mp) REVERT: C 99 ARG cc_start: 0.7381 (ptp-170) cc_final: 0.7086 (ptp90) REVERT: C 160 THR cc_start: 0.7120 (p) cc_final: 0.6662 (t) outliers start: 39 outliers final: 31 residues processed: 249 average time/residue: 0.3196 time to fit residues: 128.2303 Evaluate side-chains 244 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 212 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 389 VAL 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 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 693 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 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 624 THR 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 268 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 258 optimal weight: 3.9990 chunk 79 optimal weight: 0.2980 chunk 137 optimal weight: 0.5980 chunk 126 optimal weight: 0.0670 chunk 228 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 232 optimal weight: 0.2980 chunk 112 optimal weight: 3.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 746 ASN C 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.153489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.134854 restraints weight = 24732.607| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.43 r_work: 0.3284 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 23355 Z= 0.097 Angle : 0.514 10.014 31771 Z= 0.265 Chirality : 0.044 0.278 3659 Planarity : 0.004 0.040 4048 Dihedral : 5.113 59.695 3458 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.48 % Allowed : 10.49 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.16), residues: 2812 helix: 2.36 (0.21), residues: 649 sheet: 0.79 (0.21), residues: 662 loop : -1.67 (0.14), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 868 HIS 0.001 0.000 HIS A1046 PHE 0.013 0.001 PHE C 551 TYR 0.015 0.001 TYR C1049 ARG 0.006 0.000 ARG B 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00507 ( 18) link_NAG-ASN : angle 3.31528 ( 54) hydrogen bonds : bond 0.04998 ( 937) hydrogen bonds : angle 4.60586 ( 2589) SS BOND : bond 0.00564 ( 39) SS BOND : angle 1.98436 ( 78) covalent geometry : bond 0.00207 (23298) covalent geometry : angle 0.48663 (31639) *********************** 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 273 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 236 time to evaluate : 2.375 Fit side-chains revert: symmetry clash REVERT: A 129 ASN cc_start: 0.7435 (m110) cc_final: 0.7103 (m110) REVERT: A 183 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7648 (mtt180) REVERT: A 352 TYR cc_start: 0.8423 (m-80) cc_final: 0.7575 (m-80) REVERT: A 1032 MET cc_start: 0.8887 (ptm) cc_final: 0.8676 (ptm) REVERT: A 1074 GLU cc_start: 0.7792 (pt0) cc_final: 0.7480 (pt0) REVERT: B 99 ARG cc_start: 0.6698 (ptt180) cc_final: 0.5999 (ptp-110) REVERT: B 796 LYS cc_start: 0.8381 (mmtm) cc_final: 0.7496 (ttmt) REVERT: B 882 MET cc_start: 0.8984 (mtt) cc_final: 0.8779 (mtm) REVERT: C 903 LYS cc_start: 0.8040 (mppt) cc_final: 0.7558 (mmmt) REVERT: C 1109 ASP cc_start: 0.7571 (t0) cc_final: 0.7258 (t0) outliers start: 37 outliers final: 28 residues processed: 261 average time/residue: 0.3257 time to fit residues: 135.7498 Evaluate side-chains 244 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 215 time to evaluate : 2.566 ------------------------------------------------------------------------------- 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 183 ARG 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 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 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 539 THR Chi-restraints excluded: chain C residue 544 ARG Chi-restraints excluded: chain C residue 848 THR 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 239 optimal weight: 2.9990 chunk 252 optimal weight: 3.9990 chunk 219 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 228 optimal weight: 0.9980 chunk 260 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3566 r_free = 0.3566 target = 0.148896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.133981 restraints weight = 24760.004| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 0.79 r_work: 0.3201 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work: 0.2982 rms_B_bonded: 4.73 restraints_weight: 0.1250 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 23355 Z= 0.140 Angle : 0.563 14.350 31771 Z= 0.289 Chirality : 0.045 0.266 3659 Planarity : 0.004 0.042 4048 Dihedral : 5.248 58.522 3458 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.48 % Allowed : 11.25 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.16), residues: 2812 helix: 2.23 (0.21), residues: 650 sheet: 0.81 (0.21), residues: 661 loop : -1.68 (0.14), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 868 HIS 0.003 0.001 HIS A1046 PHE 0.018 0.001 PHE A 83 TYR 0.017 0.001 TYR C1049 ARG 0.006 0.000 ARG B 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00476 ( 18) link_NAG-ASN : angle 3.41568 ( 54) hydrogen bonds : bond 0.06199 ( 937) hydrogen bonds : angle 4.71222 ( 2589) SS BOND : bond 0.00710 ( 39) SS BOND : angle 2.28328 ( 78) covalent geometry : bond 0.00336 (23298) covalent geometry : angle 0.53458 (31639) *********************** 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 254 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 217 time to evaluate : 2.697 Fit side-chains REVERT: A 56 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8448 (tp40) REVERT: A 352 TYR cc_start: 0.8467 (m-80) cc_final: 0.7608 (m-80) REVERT: A 987 GLN cc_start: 0.8356 (mm-40) cc_final: 0.7764 (mm-40) REVERT: A 1032 MET cc_start: 0.9037 (ptm) cc_final: 0.8795 (ptm) REVERT: A 1074 GLU cc_start: 0.7849 (pt0) cc_final: 0.7554 (pt0) REVERT: B 99 ARG cc_start: 0.6853 (ptt180) cc_final: 0.6064 (ptp-110) REVERT: B 959 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8527 (mp) REVERT: C 1109 ASP cc_start: 0.7789 (t0) cc_final: 0.7391 (t0) outliers start: 37 outliers final: 32 residues processed: 243 average time/residue: 0.3479 time to fit residues: 136.0567 Evaluate side-chains 245 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 3.291 ------------------------------------------------------------------------------- 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 389 VAL 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 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 539 THR Chi-restraints excluded: chain B residue 841 THR Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 959 LEU 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 539 THR Chi-restraints excluded: chain C residue 544 ARG Chi-restraints excluded: chain C residue 848 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 148 optimal weight: 3.9990 chunk 23 optimal weight: 0.0170 chunk 64 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 278 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 0.0770 chunk 83 optimal weight: 0.5980 chunk 133 optimal weight: 0.0470 chunk 18 optimal weight: 3.9990 chunk 215 optimal weight: 0.2980 overall best weight: 0.2074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A1107 ASN B 108 ASN B 280 GLN B 357 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.154732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.131194 restraints weight = 24735.501| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.79 r_work: 0.3147 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 23355 Z= 0.089 Angle : 0.490 13.824 31771 Z= 0.252 Chirality : 0.043 0.280 3659 Planarity : 0.003 0.040 4048 Dihedral : 4.892 58.720 3458 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.60 % Allowed : 11.41 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.16), residues: 2812 helix: 2.68 (0.21), residues: 646 sheet: 0.85 (0.20), residues: 675 loop : -1.52 (0.15), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 868 HIS 0.001 0.000 HIS A1030 PHE 0.011 0.001 PHE C1103 TYR 0.015 0.001 TYR C1049 ARG 0.006 0.000 ARG B 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00510 ( 18) link_NAG-ASN : angle 3.09316 ( 54) hydrogen bonds : bond 0.04470 ( 937) hydrogen bonds : angle 4.44593 ( 2589) SS BOND : bond 0.00517 ( 39) SS BOND : angle 1.75929 ( 78) covalent geometry : bond 0.00185 (23298) covalent geometry : angle 0.46625 (31639) *********************** 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 271 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 231 time to evaluate : 2.455 Fit side-chains REVERT: A 56 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8290 (tp40) REVERT: A 183 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7663 (mtt180) REVERT: A 352 TYR cc_start: 0.8396 (m-80) cc_final: 0.7531 (m-80) REVERT: A 889 ASN cc_start: 0.7917 (t0) cc_final: 0.7384 (t0) REVERT: A 987 GLN cc_start: 0.8276 (mm-40) cc_final: 0.7716 (mm-40) REVERT: B 99 ARG cc_start: 0.6697 (ptt180) cc_final: 0.5879 (ptp-110) REVERT: C 352 TYR cc_start: 0.8084 (m-80) cc_final: 0.7797 (m-80) REVERT: C 589 ASN cc_start: 0.7821 (p0) cc_final: 0.7483 (t0) REVERT: C 903 LYS cc_start: 0.7832 (mppt) cc_final: 0.7366 (mmmt) REVERT: C 1109 ASP cc_start: 0.7753 (t0) cc_final: 0.7324 (t0) outliers start: 40 outliers final: 31 residues processed: 260 average time/residue: 0.3326 time to fit residues: 139.4448 Evaluate side-chains 250 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 217 time to evaluate : 2.567 ------------------------------------------------------------------------------- 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 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 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 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 36 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 228 optimal weight: 0.2980 chunk 278 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 215 optimal weight: 0.0970 chunk 274 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 235 optimal weight: 6.9990 chunk 190 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 108 ASN B 280 GLN B 937 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.152453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.127921 restraints weight = 24634.887| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.77 r_work: 0.2962 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 23355 Z= 0.108 Angle : 0.518 13.447 31771 Z= 0.266 Chirality : 0.044 0.273 3659 Planarity : 0.004 0.042 4048 Dihedral : 4.938 59.951 3458 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.56 % Allowed : 12.01 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.16), residues: 2812 helix: 2.65 (0.21), residues: 644 sheet: 0.95 (0.21), residues: 662 loop : -1.46 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 868 HIS 0.002 0.000 HIS C1046 PHE 0.013 0.001 PHE A 83 TYR 0.016 0.001 TYR C1049 ARG 0.007 0.000 ARG B 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00480 ( 18) link_NAG-ASN : angle 3.16344 ( 54) hydrogen bonds : bond 0.05171 ( 937) hydrogen bonds : angle 4.49151 ( 2589) SS BOND : bond 0.00580 ( 39) SS BOND : angle 1.92218 ( 78) covalent geometry : bond 0.00245 (23298) covalent geometry : angle 0.49291 (31639) *********************** 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 258 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 219 time to evaluate : 2.653 Fit side-chains REVERT: A 56 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8379 (tp40) REVERT: A 183 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7659 (mtt180) REVERT: A 352 TYR cc_start: 0.8431 (m-80) cc_final: 0.7465 (m-80) REVERT: A 889 ASN cc_start: 0.8152 (t0) cc_final: 0.7665 (t0) REVERT: A 987 GLN cc_start: 0.8365 (mm-40) cc_final: 0.7836 (mm-40) REVERT: B 99 ARG cc_start: 0.6363 (ptt180) cc_final: 0.5225 (ptp-110) REVERT: B 1032 MET cc_start: 0.9084 (ptm) cc_final: 0.8686 (ptm) REVERT: C 108 ASN cc_start: 0.7378 (m110) cc_final: 0.7116 (p0) REVERT: C 352 TYR cc_start: 0.7932 (m-80) cc_final: 0.7588 (m-80) REVERT: C 589 ASN cc_start: 0.7720 (p0) cc_final: 0.7232 (t0) REVERT: C 903 LYS cc_start: 0.7890 (mppt) cc_final: 0.7218 (mmmt) REVERT: C 1109 ASP cc_start: 0.7988 (t0) cc_final: 0.7614 (t0) outliers start: 39 outliers final: 35 residues processed: 248 average time/residue: 0.3348 time to fit residues: 135.1119 Evaluate side-chains 250 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 213 time to evaluate : 2.452 ------------------------------------------------------------------------------- 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 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 556 SER 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 914 SER Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 115 ILE 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 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 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 88 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 108 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 196 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 268 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 108 ASN B 505 ASN B 937 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.149616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.133966 restraints weight = 24949.604| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 0.83 r_work: 0.3234 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work: 0.3035 rms_B_bonded: 4.40 restraints_weight: 0.1250 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1891 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= 0.133 Angle : 0.553 13.287 31771 Z= 0.284 Chirality : 0.045 0.266 3659 Planarity : 0.004 0.042 4048 Dihedral : 5.121 58.522 3458 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.60 % Allowed : 12.17 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.16), residues: 2812 helix: 2.53 (0.21), residues: 638 sheet: 0.97 (0.21), residues: 661 loop : -1.53 (0.15), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 868 HIS 0.003 0.001 HIS C1046 PHE 0.017 0.001 PHE A 83 TYR 0.017 0.001 TYR C1049 ARG 0.006 0.000 ARG B 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00477 ( 18) link_NAG-ASN : angle 3.25450 ( 54) hydrogen bonds : bond 0.06060 ( 937) hydrogen bonds : angle 4.61975 ( 2589) SS BOND : bond 0.00637 ( 39) SS BOND : angle 2.10710 ( 78) covalent geometry : bond 0.00312 (23298) covalent geometry : angle 0.52770 (31639) *********************** 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 256 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 216 time to evaluate : 2.838 Fit side-chains REVERT: A 56 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8428 (tp40) REVERT: A 183 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7752 (mtt180) REVERT: A 352 TYR cc_start: 0.8434 (m-80) cc_final: 0.7587 (m-80) REVERT: A 987 GLN cc_start: 0.8317 (mm-40) cc_final: 0.7783 (mm-40) REVERT: B 99 ARG cc_start: 0.6879 (ptt180) cc_final: 0.6114 (ptp-110) REVERT: C 352 TYR cc_start: 0.8171 (m-80) cc_final: 0.7859 (m-80) REVERT: C 903 LYS cc_start: 0.8069 (mppt) cc_final: 0.7563 (mmmt) outliers start: 40 outliers final: 35 residues processed: 246 average time/residue: 0.3254 time to fit residues: 129.4184 Evaluate side-chains 246 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 209 time to evaluate : 2.395 ------------------------------------------------------------------------------- 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 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 556 SER 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 914 SER Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain B residue 115 ILE 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 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 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 250 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 190 optimal weight: 0.5980 chunk 286 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 63 optimal weight: 0.4980 chunk 216 optimal weight: 0.8980 chunk 160 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3578 r_free = 0.3578 target = 0.149788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.122721 restraints weight = 24885.893| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.03 r_work: 0.2954 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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= 0.132 Angle : 0.556 13.167 31771 Z= 0.286 Chirality : 0.045 0.266 3659 Planarity : 0.004 0.043 4048 Dihedral : 5.173 58.490 3458 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % 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 : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.16), residues: 2812 helix: 2.45 (0.21), residues: 638 sheet: 0.98 (0.21), residues: 650 loop : -1.53 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 868 HIS 0.003 0.001 HIS C1046 PHE 0.016 0.001 PHE A 83 TYR 0.017 0.001 TYR C1049 ARG 0.007 0.000 ARG B 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00468 ( 18) link_NAG-ASN : angle 3.25524 ( 54) hydrogen bonds : bond 0.06051 ( 937) hydrogen bonds : angle 4.64011 ( 2589) SS BOND : bond 0.00636 ( 39) SS BOND : angle 2.13008 ( 78) covalent geometry : bond 0.00310 (23298) covalent geometry : angle 0.53045 (31639) ********************** 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 249 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 209 time to evaluate : 2.515 Fit side-chains REVERT: A 56 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8358 (tp40) REVERT: A 183 ARG cc_start: 0.7972 (ptp-170) cc_final: 0.7681 (mtt180) REVERT: A 352 TYR cc_start: 0.8450 (m-80) cc_final: 0.7524 (m-80) REVERT: A 987 GLN cc_start: 0.8387 (mm-40) cc_final: 0.7853 (mm-40) REVERT: B 99 ARG cc_start: 0.6478 (ptt180) cc_final: 0.5321 (ptp-110) REVERT: B 635 CYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7677 (p) REVERT: C 352 TYR cc_start: 0.7926 (m-80) cc_final: 0.7583 (m-80) REVERT: C 799 PHE cc_start: 0.7670 (t80) cc_final: 0.7456 (t80) REVERT: C 903 LYS cc_start: 0.7886 (mppt) cc_final: 0.7266 (mmmt) outliers start: 40 outliers final: 38 residues processed: 242 average time/residue: 0.3300 time to fit residues: 129.9379 Evaluate side-chains 247 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 207 time to evaluate : 2.505 ------------------------------------------------------------------------------- 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 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 556 SER 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 115 ILE 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 537 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 635 CYS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 95 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 275 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3552 r_free = 0.3552 target = 0.147534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.132476 restraints weight = 24759.925| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 0.81 r_work: 0.3223 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 23355 Z= 0.162 Angle : 0.597 13.293 31771 Z= 0.306 Chirality : 0.047 0.263 3659 Planarity : 0.004 0.043 4048 Dihedral : 5.380 59.559 3458 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.68 % Allowed : 12.29 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.16), residues: 2812 helix: 2.21 (0.21), residues: 636 sheet: 1.02 (0.21), residues: 651 loop : -1.61 (0.14), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 868 HIS 0.004 0.001 HIS C1046 PHE 0.019 0.002 PHE A 83 TYR 0.017 0.001 TYR C1049 ARG 0.006 0.000 ARG B 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00457 ( 18) link_NAG-ASN : angle 3.39375 ( 54) hydrogen bonds : bond 0.06858 ( 937) hydrogen bonds : angle 4.77772 ( 2589) SS BOND : bond 0.00712 ( 39) SS BOND : angle 2.36246 ( 78) covalent geometry : bond 0.00393 (23298) covalent geometry : angle 0.56995 (31639) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10949.62 seconds wall clock time: 190 minutes 7.03 seconds (11407.03 seconds total)