Starting phenix.real_space_refine on Wed Mar 4 21:38:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7crw_30458/03_2026/7crw_30458.cif Found real_map, /net/cci-nas-00/data/ceres_data/7crw_30458/03_2026/7crw_30458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7crw_30458/03_2026/7crw_30458.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7crw_30458/03_2026/7crw_30458.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7crw_30458/03_2026/7crw_30458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7crw_30458/03_2026/7crw_30458.map" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 79 5.16 5 C 10687 2.51 5 N 2832 2.21 5 O 3015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16613 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 6765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 837, 6765 Classifications: {'peptide': 837} Link IDs: {'PTRANS': 53, 'TRANS': 783} Chain breaks: 1 Chain: "A" Number of atoms: 2225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2225 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 258} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1096 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "C" Number of atoms: 6527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 807, 6527 Classifications: {'peptide': 807} Link IDs: {'PTRANS': 53, 'TRANS': 753} Chain breaks: 5 Time building chain proxies: 3.73, per 1000 atoms: 0.22 Number of scatterers: 16613 At special positions: 0 Unit cell: (103.978, 149.601, 113.527, 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 79 16.00 O 3015 8.00 N 2832 7.00 C 10687 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 741.0 milliseconds 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3860 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 35 sheets defined 18.6% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'D' and resid 29 through 43 Processing helix chain 'D' and resid 61 through 65 removed outlier: 3.500A pdb=" N GLY D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 119 Processing helix chain 'D' and resid 121 through 132 Processing helix chain 'D' and resid 242 through 249 Processing helix chain 'D' and resid 340 through 345 Processing helix chain 'D' and resid 381 through 383 No H-bonds generated for 'chain 'D' and resid 381 through 383' Processing helix chain 'D' and resid 391 through 402 removed outlier: 3.548A pdb=" N GLU D 397 " --> pdb=" O ALA D 393 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG D 400 " --> pdb=" O GLN D 396 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE D 402 " --> pdb=" O ALA D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 661 through 670 Processing helix chain 'D' and resid 685 through 690 removed outlier: 3.765A pdb=" N GLU D 689 " --> pdb=" O GLY D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 715 removed outlier: 3.785A pdb=" N ASP D 703 " --> pdb=" O VAL D 699 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL D 711 " --> pdb=" O GLY D 707 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA D 712 " --> pdb=" O LEU D 708 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU D 713 " --> pdb=" O GLN D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 730 through 742 Processing helix chain 'D' and resid 757 through 761 removed outlier: 3.818A pdb=" N ALA D 760 " --> pdb=" O VAL D 757 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR D 761 " --> pdb=" O TRP D 758 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 757 through 761' Processing helix chain 'D' and resid 762 through 771 removed outlier: 4.623A pdb=" N ARG D 768 " --> pdb=" O GLY D 764 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 784 removed outlier: 3.557A pdb=" N ASN D 776 " --> pdb=" O VAL D 772 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N GLN D 778 " --> pdb=" O GLU D 774 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY D 779 " --> pdb=" O ASN D 775 " (cutoff:3.500A) Processing helix chain 'D' and resid 785 through 792 removed outlier: 4.098A pdb=" N VAL D 789 " --> pdb=" O ALA D 786 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLU D 790 " --> pdb=" O LEU D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 812 through 824 Processing helix chain 'D' and resid 843 through 862 Processing helix chain 'A' and resid 887 through 893 removed outlier: 4.166A pdb=" N PHE A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 900 removed outlier: 3.655A pdb=" N HIS A 899 " --> pdb=" O PRO A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 915 No H-bonds generated for 'chain 'A' and resid 913 through 915' Processing helix chain 'A' and resid 1012 through 1025 Processing helix chain 'B' and resid 1013 through 1025 removed outlier: 3.609A pdb=" N LYS B1017 " --> pdb=" O CYS B1013 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU B1021 " --> pdb=" O LYS B1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 43 Processing helix chain 'C' and resid 242 through 249 Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 340 through 345 Processing helix chain 'C' and resid 381 through 383 No H-bonds generated for 'chain 'C' and resid 381 through 383' Processing helix chain 'C' and resid 391 through 399 removed outlier: 3.573A pdb=" N GLN C 396 " --> pdb=" O GLU C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 670 removed outlier: 3.747A pdb=" N GLY C 670 " --> pdb=" O LEU C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 692 removed outlier: 3.684A pdb=" N LEU C 692 " --> pdb=" O GLU C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 715 removed outlier: 3.601A pdb=" N ASP C 703 " --> pdb=" O VAL C 699 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR C 710 " --> pdb=" O GLU C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 742 Processing helix chain 'C' and resid 757 through 761 removed outlier: 3.802A pdb=" N ALA C 760 " --> pdb=" O VAL C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 771 removed outlier: 4.218A pdb=" N ARG C 768 " --> pdb=" O GLY C 764 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR C 769 " --> pdb=" O TYR C 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 775 Processing helix chain 'C' and resid 776 through 782 removed outlier: 4.131A pdb=" N GLU C 781 " --> pdb=" O GLN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 792 removed outlier: 4.540A pdb=" N VAL C 789 " --> pdb=" O ALA C 786 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLU C 790 " --> pdb=" O LEU C 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 825 removed outlier: 3.923A pdb=" N ARG C 824 " --> pdb=" O SER C 820 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA C 825 " --> pdb=" O GLN C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 862 removed outlier: 3.747A pdb=" N THR C 853 " --> pdb=" O HIS C 849 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 56 through 59 removed outlier: 3.726A pdb=" N HIS D 69 " --> pdb=" O ILE D 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 99 through 102 removed outlier: 3.546A pdb=" N LEU D 99 " --> pdb=" O LEU A 950 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 142 through 144 Processing sheet with id=AA4, first strand: chain 'D' and resid 188 through 192 removed outlier: 6.503A pdb=" N SER D 201 " --> pdb=" O PRO D 190 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ILE D 192 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE D 199 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 236 through 238 Processing sheet with id=AA6, first strand: chain 'D' and resid 236 through 238 Processing sheet with id=AA7, first strand: chain 'D' and resid 270 through 272 removed outlier: 6.532A pdb=" N GLN D 322 " --> pdb=" O VAL D 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 286 through 290 Processing sheet with id=AA9, first strand: chain 'D' and resid 335 through 337 Processing sheet with id=AB1, first strand: chain 'D' and resid 350 through 356 removed outlier: 5.738A pdb=" N ILE D 351 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU D 368 " --> pdb=" O ILE D 351 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG D 353 " --> pdb=" O MET D 366 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU D 375 " --> pdb=" O GLU D 413 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU D 413 " --> pdb=" O LEU D 375 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU D 377 " --> pdb=" O ILE D 411 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 426 through 428 removed outlier: 6.518A pdb=" N ASP D 459 " --> pdb=" O ILE D 482 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE D 482 " --> pdb=" O ASP D 459 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 504 through 506 Processing sheet with id=AB4, first strand: chain 'D' and resid 546 through 551 removed outlier: 3.513A pdb=" N SER D 563 " --> pdb=" O SER D 546 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N SER D 564 " --> pdb=" O PRO D 568 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL D 571 " --> pdb=" O MET D 594 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS D 575 " --> pdb=" O PHE D 590 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N PHE D 590 " --> pdb=" O LYS D 575 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N SER D 577 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 608 through 613 removed outlier: 4.561A pdb=" N TYR D 621 " --> pdb=" O ASP D 677 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP D 677 " --> pdb=" O TYR D 621 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL D 673 " --> pdb=" O TYR D 625 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N VAL D 674 " --> pdb=" O PRO D 637 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL D 639 " --> pdb=" O VAL D 674 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ILE D 676 " --> pdb=" O VAL D 639 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N PHE D 641 " --> pdb=" O ILE D 676 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N HIS D 636 " --> pdb=" O ASP D 719 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N SER D 721 " --> pdb=" O HIS D 636 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N THR D 638 " --> pdb=" O SER D 721 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL D 723 " --> pdb=" O THR D 638 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU D 640 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ILE D 725 " --> pdb=" O LEU D 640 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 750 through 752 removed outlier: 6.379A pdb=" N ILE D 801 " --> pdb=" O GLN D 832 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N TYR D 834 " --> pdb=" O ILE D 801 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N HIS D 803 " --> pdb=" O TYR D 834 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 845 through 848 removed outlier: 4.194A pdb=" N GLU A 845 " --> pdb=" O ARG A 855 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU A 853 " --> pdb=" O VAL A 847 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 862 through 866 removed outlier: 4.052A pdb=" N ARG A 955 " --> pdb=" O VAL A 962 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 986 through 987 removed outlier: 3.518A pdb=" N LEU A1040 " --> pdb=" O ILE A 987 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1029 through 1031 removed outlier: 4.163A pdb=" N ILE A 993 " --> pdb=" O ILE A1031 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A1055 " --> pdb=" O TYR A1078 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1060 through 1062 removed outlier: 3.707A pdb=" N TRP A1100 " --> pdb=" O LEU A1090 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASP A1092 " --> pdb=" O LEU A1098 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU A1098 " --> pdb=" O ASP A1092 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1029 through 1031 removed outlier: 4.133A pdb=" N ILE B 993 " --> pdb=" O ILE B1031 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 1060 through 1062 Processing sheet with id=AC5, first strand: chain 'C' and resid 56 through 59 removed outlier: 6.812A pdb=" N ILE C 90 " --> pdb=" O SER C 68 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARG C 70 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N SER C 88 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR C 72 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU C 86 " --> pdb=" O TYR C 72 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU C 74 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N SER C 84 " --> pdb=" O LEU C 74 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 142 through 144 Processing sheet with id=AC7, first strand: chain 'C' and resid 188 through 193 removed outlier: 6.575A pdb=" N SER C 201 " --> pdb=" O PRO C 190 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ILE C 192 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N PHE C 199 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 236 through 238 Processing sheet with id=AC9, first strand: chain 'C' and resid 236 through 238 Processing sheet with id=AD1, first strand: chain 'C' and resid 270 through 272 removed outlier: 6.551A pdb=" N GLN C 322 " --> pdb=" O VAL C 330 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 286 through 290 Processing sheet with id=AD3, first strand: chain 'C' and resid 335 through 337 Processing sheet with id=AD4, first strand: chain 'C' and resid 350 through 356 removed outlier: 5.459A pdb=" N ILE C 351 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU C 368 " --> pdb=" O ILE C 351 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG C 353 " --> pdb=" O MET C 366 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 426 through 428 removed outlier: 6.759A pdb=" N ARG C 455 " --> pdb=" O GLU C 485 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLU C 485 " --> pdb=" O ARG C 455 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR C 457 " --> pdb=" O LYS C 483 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 504 through 506 Processing sheet with id=AD7, first strand: chain 'C' and resid 546 through 551 removed outlier: 3.643A pdb=" N HIS C 561 " --> pdb=" O SER C 548 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL C 559 " --> pdb=" O SER C 550 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N SER C 564 " --> pdb=" O PRO C 568 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL C 571 " --> pdb=" O SER C 593 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N SER C 593 " --> pdb=" O VAL C 571 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL C 573 " --> pdb=" O TRP C 591 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN C 587 " --> pdb=" O SER C 577 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 608 through 613 removed outlier: 4.175A pdb=" N TYR C 621 " --> pdb=" O ASP C 677 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C 673 " --> pdb=" O TYR C 625 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N VAL C 674 " --> pdb=" O PRO C 637 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL C 639 " --> pdb=" O VAL C 674 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ILE C 676 " --> pdb=" O VAL C 639 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N PHE C 641 " --> pdb=" O ILE C 676 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N HIS C 636 " --> pdb=" O ASP C 719 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N SER C 721 " --> pdb=" O HIS C 636 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N THR C 638 " --> pdb=" O SER C 721 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL C 723 " --> pdb=" O THR C 638 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU C 640 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE C 725 " --> pdb=" O LEU C 640 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ILE C 750 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE C 725 " --> pdb=" O ILE C 750 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N GLY C 752 " --> pdb=" O ILE C 725 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY C 727 " --> pdb=" O GLY C 752 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA C 749 " --> pdb=" O LEU C 800 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N LEU C 802 " --> pdb=" O ALA C 749 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA C 751 " --> pdb=" O LEU C 802 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N GLY C 804 " --> pdb=" O ALA C 751 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N GLN C 832 " --> pdb=" O LEU C 799 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE C 801 " --> pdb=" O GLN C 832 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N TYR C 834 " --> pdb=" O ILE C 801 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N HIS C 803 " --> pdb=" O TYR C 834 " (cutoff:3.500A) 520 hydrogen bonds defined for protein. 1347 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: 3.88 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3858 1.33 - 1.45: 3786 1.45 - 1.57: 9339 1.57 - 1.69: 0 1.69 - 1.81: 117 Bond restraints: 17100 Sorted by residual: bond pdb=" N CYS C 600 " pdb=" CA CYS C 600 " ideal model delta sigma weight residual 1.457 1.496 -0.039 9.10e-03 1.21e+04 1.86e+01 bond pdb=" C THR C 567 " pdb=" N PRO C 568 " ideal model delta sigma weight residual 1.329 1.371 -0.042 1.18e-02 7.18e+03 1.27e+01 bond pdb=" N ILE A1082 " pdb=" CA ILE A1082 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.07e-02 8.73e+03 1.03e+01 bond pdb=" N ASP D 603 " pdb=" CA ASP D 603 " ideal model delta sigma weight residual 1.459 1.488 -0.029 9.10e-03 1.21e+04 9.95e+00 bond pdb=" C CYS C 600 " pdb=" O CYS C 600 " ideal model delta sigma weight residual 1.233 1.248 -0.015 4.80e-03 4.34e+04 9.61e+00 ... (remaining 17095 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 23046 3.07 - 6.13: 166 6.13 - 9.20: 7 9.20 - 12.27: 2 12.27 - 15.33: 2 Bond angle restraints: 23223 Sorted by residual: angle pdb=" N PRO C 601 " pdb=" CA PRO C 601 " pdb=" C PRO C 601 " ideal model delta sigma weight residual 110.70 126.03 -15.33 1.22e+00 6.72e-01 1.58e+02 angle pdb=" N PRO D 601 " pdb=" CA PRO D 601 " pdb=" C PRO D 601 " ideal model delta sigma weight residual 110.70 125.22 -14.52 1.22e+00 6.72e-01 1.42e+02 angle pdb=" N ILE A1082 " pdb=" CA ILE A1082 " pdb=" C ILE A1082 " ideal model delta sigma weight residual 113.10 105.42 7.68 9.70e-01 1.06e+00 6.27e+01 angle pdb=" N PRO C 602 " pdb=" CA PRO C 602 " pdb=" C PRO C 602 " ideal model delta sigma weight residual 112.47 124.58 -12.11 2.06e+00 2.36e-01 3.46e+01 angle pdb=" N VAL A 981 " pdb=" CA VAL A 981 " pdb=" C VAL A 981 " ideal model delta sigma weight residual 113.71 108.53 5.18 9.50e-01 1.11e+00 2.97e+01 ... (remaining 23218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 9010 15.94 - 31.89: 901 31.89 - 47.83: 170 47.83 - 63.78: 39 63.78 - 79.72: 17 Dihedral angle restraints: 10137 sinusoidal: 4141 harmonic: 5996 Sorted by residual: dihedral pdb=" CA ALA C 154 " pdb=" C ALA C 154 " pdb=" N SER C 155 " pdb=" CA SER C 155 " ideal model delta harmonic sigma weight residual 180.00 150.72 29.28 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA SER C 729 " pdb=" C SER C 729 " pdb=" N TYR C 730 " pdb=" CA TYR C 730 " ideal model delta harmonic sigma weight residual 180.00 154.81 25.19 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA VAL C 772 " pdb=" C VAL C 772 " pdb=" N PRO C 773 " pdb=" CA PRO C 773 " ideal model delta harmonic sigma weight residual -180.00 -156.19 -23.81 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 10134 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 2386 0.111 - 0.222: 69 0.222 - 0.334: 9 0.334 - 0.445: 2 0.445 - 0.556: 2 Chirality restraints: 2468 Sorted by residual: chirality pdb=" CA PRO C 601 " pdb=" N PRO C 601 " pdb=" C PRO C 601 " pdb=" CB PRO C 601 " both_signs ideal model delta sigma weight residual False 2.72 2.16 0.56 2.00e-01 2.50e+01 7.73e+00 chirality pdb=" CA PRO D 601 " pdb=" N PRO D 601 " pdb=" C PRO D 601 " pdb=" CB PRO D 601 " both_signs ideal model delta sigma weight residual False 2.72 2.23 0.49 2.00e-01 2.50e+01 6.07e+00 chirality pdb=" CA LEU A1057 " pdb=" N LEU A1057 " pdb=" C LEU A1057 " pdb=" CB LEU A1057 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 2465 not shown) Planarity restraints: 3007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 599 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.04e+00 pdb=" C SER D 599 " 0.052 2.00e-02 2.50e+03 pdb=" O SER D 599 " -0.020 2.00e-02 2.50e+03 pdb=" N CYS D 600 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A1077 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.62e+00 pdb=" C ILE A1077 " 0.051 2.00e-02 2.50e+03 pdb=" O ILE A1077 " -0.019 2.00e-02 2.50e+03 pdb=" N TYR A1078 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A1056 " 0.014 2.00e-02 2.50e+03 2.72e-02 7.42e+00 pdb=" C ILE A1056 " -0.047 2.00e-02 2.50e+03 pdb=" O ILE A1056 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU A1057 " 0.016 2.00e-02 2.50e+03 ... (remaining 3004 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1593 2.74 - 3.28: 15985 3.28 - 3.82: 26760 3.82 - 4.36: 33296 4.36 - 4.90: 56843 Nonbonded interactions: 134477 Sorted by model distance: nonbonded pdb=" NH1 ARG D 251 " pdb=" O ILE D 351 " model vdw 2.202 3.120 nonbonded pdb=" NH1 ARG C 219 " pdb=" OG SER C 332 " model vdw 2.227 3.120 nonbonded pdb=" OG SER A 989 " pdb=" O VAL A1009 " model vdw 2.228 3.040 nonbonded pdb=" O ARG D 306 " pdb=" OG SER D 309 " model vdw 2.245 3.040 nonbonded pdb=" OH TYR C 72 " pdb=" OD2 ASP C 163 " model vdw 2.249 3.040 ... (remaining 134472 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 'C' selection = (chain 'D' and (resid 21 through 44 or resid 50 through 62 or resid 65 through 1 \ 15 or resid 136 through 227 or resid 231 through 862)) } 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=0.38 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: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.980 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 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 : 0.005 0.042 17100 Z= 0.283 Angle : 0.732 15.334 23223 Z= 0.468 Chirality : 0.053 0.556 2468 Planarity : 0.004 0.038 3007 Dihedral : 13.491 79.722 6277 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.94 % Favored : 93.91 % Rotamer: Outliers : 0.60 % Allowed : 5.16 % Favored : 94.24 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.70 (0.16), residues: 2037 helix: -3.08 (0.20), residues: 319 sheet: -2.21 (0.19), residues: 636 loop : -2.39 (0.17), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 187 TYR 0.014 0.002 TYR D 531 PHE 0.014 0.001 PHE A 960 TRP 0.011 0.001 TRP C 419 HIS 0.006 0.001 HIS C 803 Details of bonding type rmsd covalent geometry : bond 0.00489 (17100) covalent geometry : angle 0.73221 (23223) hydrogen bonds : bond 0.22122 ( 516) hydrogen bonds : angle 8.78793 ( 1347) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 179 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 860 MET cc_start: 0.7470 (ptt) cc_final: 0.6660 (pmm) REVERT: A 898 GLN cc_start: 0.8371 (pp30) cc_final: 0.7946 (pp30) REVERT: A 948 MET cc_start: 0.8233 (ttp) cc_final: 0.7974 (ttt) REVERT: A 1046 TYR cc_start: 0.8501 (m-80) cc_final: 0.7783 (m-80) REVERT: A 1084 SER cc_start: 0.8745 (m) cc_final: 0.8476 (t) REVERT: A 1093 LYS cc_start: 0.9035 (ttpt) cc_final: 0.8616 (ttmm) REVERT: C 188 MET cc_start: 0.7926 (mtp) cc_final: 0.7663 (mtm) REVERT: C 250 ASP cc_start: 0.7341 (t0) cc_final: 0.7101 (t0) outliers start: 11 outliers final: 2 residues processed: 185 average time/residue: 0.1525 time to fit residues: 40.5373 Evaluate side-chains 118 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1079 VAL Chi-restraints excluded: chain C residue 573 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 69 HIS D 117 HIS D 160 HIS D 204 ASN D 506 ASN D 515 GLN D 547 HIS ** D 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 HIS D 647 GLN D 649 GLN D 803 HIS D 859 GLN A 852 ASN A 929 GLN A1089 GLN ** A1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1089 GLN C 69 HIS ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 ASN C 311 ASN C 339 GLN C 803 HIS C 839 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.082521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.065574 restraints weight = 42558.127| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.05 r_work: 0.2988 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17100 Z= 0.157 Angle : 0.619 15.488 23223 Z= 0.321 Chirality : 0.045 0.193 2468 Planarity : 0.005 0.042 3007 Dihedral : 5.280 48.909 2238 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.06 % Favored : 94.89 % Rotamer: Outliers : 1.59 % Allowed : 9.17 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.17), residues: 2037 helix: -1.42 (0.26), residues: 322 sheet: -1.70 (0.19), residues: 635 loop : -1.88 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 95 TYR 0.021 0.002 TYR A 998 PHE 0.014 0.001 PHE B1004 TRP 0.009 0.001 TRP C 395 HIS 0.005 0.001 HIS A 946 Details of bonding type rmsd covalent geometry : bond 0.00360 (17100) covalent geometry : angle 0.61891 (23223) hydrogen bonds : bond 0.04313 ( 516) hydrogen bonds : angle 5.96403 ( 1347) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 898 GLN cc_start: 0.8820 (pp30) cc_final: 0.8480 (pp30) REVERT: A 948 MET cc_start: 0.8784 (ttp) cc_final: 0.8523 (ttt) REVERT: A 1084 SER cc_start: 0.8919 (m) cc_final: 0.8598 (t) REVERT: B 1105 LYS cc_start: 0.9098 (mttp) cc_final: 0.8886 (mttp) REVERT: C 188 MET cc_start: 0.7724 (mtp) cc_final: 0.7490 (mtm) REVERT: C 250 ASP cc_start: 0.8029 (t0) cc_final: 0.7746 (t0) REVERT: C 595 MET cc_start: 0.7734 (ttp) cc_final: 0.7437 (ttp) outliers start: 29 outliers final: 12 residues processed: 141 average time/residue: 0.1553 time to fit residues: 32.2788 Evaluate side-chains 123 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1097 ASN Chi-restraints excluded: chain B residue 1009 VAL Chi-restraints excluded: chain B residue 1014 THR Chi-restraints excluded: chain B residue 1097 ASN Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 810 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 36 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 173 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 131 optimal weight: 0.0770 chunk 95 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 overall best weight: 2.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 983 HIS ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 GLN C 547 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.081956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.064640 restraints weight = 43413.759| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.12 r_work: 0.2967 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17100 Z= 0.173 Angle : 0.592 14.450 23223 Z= 0.306 Chirality : 0.045 0.195 2468 Planarity : 0.004 0.048 3007 Dihedral : 5.062 30.649 2236 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.45 % Favored : 94.50 % Rotamer: Outliers : 1.59 % Allowed : 12.02 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.18), residues: 2037 helix: -0.91 (0.28), residues: 323 sheet: -1.39 (0.20), residues: 643 loop : -1.63 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 95 TYR 0.014 0.001 TYR D 625 PHE 0.015 0.001 PHE C 688 TRP 0.008 0.001 TRP D 257 HIS 0.005 0.001 HIS A 946 Details of bonding type rmsd covalent geometry : bond 0.00403 (17100) covalent geometry : angle 0.59157 (23223) hydrogen bonds : bond 0.03992 ( 516) hydrogen bonds : angle 5.55915 ( 1347) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 898 GLN cc_start: 0.8862 (pp30) cc_final: 0.8512 (pp30) REVERT: A 948 MET cc_start: 0.8757 (ttp) cc_final: 0.8487 (ttt) REVERT: A 1084 SER cc_start: 0.8873 (m) cc_final: 0.8546 (t) REVERT: B 1105 LYS cc_start: 0.9128 (mttp) cc_final: 0.8893 (mttp) REVERT: C 188 MET cc_start: 0.7694 (mtp) cc_final: 0.7460 (mtm) REVERT: C 250 ASP cc_start: 0.8104 (t0) cc_final: 0.7790 (t0) REVERT: C 595 MET cc_start: 0.8002 (ttp) cc_final: 0.7682 (ttp) outliers start: 29 outliers final: 21 residues processed: 142 average time/residue: 0.1443 time to fit residues: 30.9224 Evaluate side-chains 132 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 890 GLN Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1089 GLN Chi-restraints excluded: chain A residue 1097 ASN Chi-restraints excluded: chain B residue 1009 VAL Chi-restraints excluded: chain B residue 1013 CYS Chi-restraints excluded: chain B residue 1014 THR Chi-restraints excluded: chain B residue 1031 ILE Chi-restraints excluded: chain B residue 1097 ASN Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain C residue 623 MET Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 810 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 125 optimal weight: 20.0000 chunk 64 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 123 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 GLN ** D 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 704 GLN ** A1097 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.082866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.065701 restraints weight = 42967.160| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.10 r_work: 0.2989 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17100 Z= 0.136 Angle : 0.566 13.429 23223 Z= 0.291 Chirality : 0.044 0.195 2468 Planarity : 0.004 0.050 3007 Dihedral : 4.891 30.913 2236 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.01 % Favored : 94.94 % Rotamer: Outliers : 2.03 % Allowed : 13.01 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.18), residues: 2037 helix: -0.49 (0.29), residues: 318 sheet: -1.11 (0.20), residues: 632 loop : -1.38 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 95 TYR 0.017 0.001 TYR A 998 PHE 0.013 0.001 PHE C 688 TRP 0.008 0.001 TRP C 257 HIS 0.005 0.001 HIS A 946 Details of bonding type rmsd covalent geometry : bond 0.00314 (17100) covalent geometry : angle 0.56562 (23223) hydrogen bonds : bond 0.03522 ( 516) hydrogen bonds : angle 5.31819 ( 1347) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 53 HIS cc_start: 0.8146 (m-70) cc_final: 0.7608 (m170) REVERT: D 278 GLU cc_start: 0.8272 (tt0) cc_final: 0.7870 (tm-30) REVERT: D 379 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8481 (mp) REVERT: A 836 TRP cc_start: 0.8236 (m100) cc_final: 0.7837 (m100) REVERT: A 898 GLN cc_start: 0.8861 (pp30) cc_final: 0.8504 (pp30) REVERT: A 948 MET cc_start: 0.8766 (ttp) cc_final: 0.8451 (ttt) REVERT: A 1084 SER cc_start: 0.8823 (m) cc_final: 0.8477 (t) REVERT: A 1089 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8272 (mt0) REVERT: B 1105 LYS cc_start: 0.9084 (mttp) cc_final: 0.8824 (mttp) REVERT: C 174 MET cc_start: 0.7825 (mmt) cc_final: 0.7623 (mmm) REVERT: C 188 MET cc_start: 0.7652 (mtp) cc_final: 0.7413 (mtm) REVERT: C 250 ASP cc_start: 0.8065 (t0) cc_final: 0.7738 (t0) REVERT: C 595 MET cc_start: 0.8043 (ttp) cc_final: 0.7770 (ttp) outliers start: 37 outliers final: 21 residues processed: 150 average time/residue: 0.1368 time to fit residues: 31.7086 Evaluate side-chains 141 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 549 CYS Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 642 VAL Chi-restraints excluded: chain A residue 860 MET Chi-restraints excluded: chain A residue 865 HIS Chi-restraints excluded: chain A residue 890 GLN Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1089 GLN Chi-restraints excluded: chain B residue 1009 VAL Chi-restraints excluded: chain B residue 1013 CYS Chi-restraints excluded: chain B residue 1014 THR Chi-restraints excluded: chain B residue 1031 ILE Chi-restraints excluded: chain B residue 1097 ASN Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 623 MET Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 810 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 32 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 161 optimal weight: 7.9990 chunk 184 optimal weight: 0.0000 chunk 166 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 116 optimal weight: 0.6980 chunk 135 optimal weight: 6.9990 chunk 39 optimal weight: 0.0370 chunk 113 optimal weight: 10.0000 overall best weight: 0.7064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 59 GLN A 929 GLN ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.084113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.067218 restraints weight = 42183.903| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.07 r_work: 0.3025 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17100 Z= 0.099 Angle : 0.537 13.888 23223 Z= 0.275 Chirality : 0.043 0.196 2468 Planarity : 0.004 0.050 3007 Dihedral : 4.656 31.394 2236 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.65 % Allowed : 14.05 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.18), residues: 2037 helix: -0.05 (0.30), residues: 317 sheet: -0.85 (0.21), residues: 635 loop : -1.22 (0.18), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 95 TYR 0.014 0.001 TYR C 513 PHE 0.011 0.001 PHE C 688 TRP 0.007 0.001 TRP C 209 HIS 0.004 0.001 HIS A 946 Details of bonding type rmsd covalent geometry : bond 0.00223 (17100) covalent geometry : angle 0.53664 (23223) hydrogen bonds : bond 0.03143 ( 516) hydrogen bonds : angle 5.10144 ( 1347) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 53 HIS cc_start: 0.8158 (m-70) cc_final: 0.7643 (m170) REVERT: D 379 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8452 (mp) REVERT: A 836 TRP cc_start: 0.8140 (m100) cc_final: 0.7770 (m100) REVERT: A 898 GLN cc_start: 0.8871 (pp30) cc_final: 0.8533 (pp30) REVERT: A 1084 SER cc_start: 0.8817 (m) cc_final: 0.8492 (t) REVERT: A 1089 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8246 (mt0) REVERT: B 1020 ASP cc_start: 0.8699 (t0) cc_final: 0.8099 (m-30) REVERT: B 1105 LYS cc_start: 0.9059 (mttp) cc_final: 0.8806 (mttp) REVERT: C 250 ASP cc_start: 0.8034 (t0) cc_final: 0.7695 (t0) REVERT: C 595 MET cc_start: 0.8074 (ttp) cc_final: 0.7810 (ttp) REVERT: C 695 GLN cc_start: 0.8477 (mt0) cc_final: 0.8276 (mt0) outliers start: 30 outliers final: 19 residues processed: 149 average time/residue: 0.1319 time to fit residues: 30.4256 Evaluate side-chains 142 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 549 CYS Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 860 MET Chi-restraints excluded: chain A residue 865 HIS Chi-restraints excluded: chain A residue 890 GLN Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 971 MET Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1089 GLN Chi-restraints excluded: chain B residue 1009 VAL Chi-restraints excluded: chain B residue 1054 VAL Chi-restraints excluded: chain B residue 1097 ASN Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 623 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 118 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 135 optimal weight: 0.0470 overall best weight: 0.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.084343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.067436 restraints weight = 42179.933| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.07 r_work: 0.3030 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17100 Z= 0.105 Angle : 0.541 16.656 23223 Z= 0.276 Chirality : 0.043 0.196 2468 Planarity : 0.004 0.053 3007 Dihedral : 4.543 31.191 2236 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.20 % Allowed : 14.38 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.19), residues: 2037 helix: 0.20 (0.30), residues: 318 sheet: -0.70 (0.21), residues: 643 loop : -1.12 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 95 TYR 0.014 0.001 TYR B1046 PHE 0.012 0.001 PHE C 688 TRP 0.007 0.001 TRP A 888 HIS 0.003 0.001 HIS A 872 Details of bonding type rmsd covalent geometry : bond 0.00240 (17100) covalent geometry : angle 0.54052 (23223) hydrogen bonds : bond 0.03076 ( 516) hydrogen bonds : angle 4.97211 ( 1347) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 53 HIS cc_start: 0.8169 (m-70) cc_final: 0.7647 (m170) REVERT: D 379 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8455 (mp) REVERT: A 836 TRP cc_start: 0.8030 (m100) cc_final: 0.7695 (m100) REVERT: A 898 GLN cc_start: 0.8861 (pp30) cc_final: 0.8563 (pp30) REVERT: A 1084 SER cc_start: 0.8758 (m) cc_final: 0.8393 (t) REVERT: A 1088 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8604 (mp) REVERT: A 1105 LYS cc_start: 0.8065 (mttp) cc_final: 0.7738 (mmtm) REVERT: B 1020 ASP cc_start: 0.8700 (t0) cc_final: 0.8080 (m-30) REVERT: C 250 ASP cc_start: 0.8000 (t0) cc_final: 0.7669 (t0) REVERT: C 595 MET cc_start: 0.8132 (ttp) cc_final: 0.7875 (ttp) outliers start: 40 outliers final: 26 residues processed: 148 average time/residue: 0.1334 time to fit residues: 30.7075 Evaluate side-chains 141 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 549 CYS Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 860 MET Chi-restraints excluded: chain A residue 865 HIS Chi-restraints excluded: chain A residue 890 GLN Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 1025 LYS Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1082 ILE Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1089 GLN Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain B residue 1009 VAL Chi-restraints excluded: chain B residue 1013 CYS Chi-restraints excluded: chain B residue 1054 VAL Chi-restraints excluded: chain B residue 1097 ASN Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 623 MET Chi-restraints excluded: chain C residue 810 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 119 optimal weight: 0.7980 chunk 143 optimal weight: 0.2980 chunk 3 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 195 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 929 GLN ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.084884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.068110 restraints weight = 42006.941| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 3.07 r_work: 0.3044 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17100 Z= 0.098 Angle : 0.533 15.448 23223 Z= 0.271 Chirality : 0.043 0.199 2468 Planarity : 0.004 0.055 3007 Dihedral : 4.455 31.254 2236 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.14 % Allowed : 14.38 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.19), residues: 2037 helix: 0.39 (0.30), residues: 318 sheet: -0.55 (0.21), residues: 644 loop : -1.03 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 95 TYR 0.014 0.001 TYR B1046 PHE 0.011 0.001 PHE C 688 TRP 0.008 0.001 TRP C 758 HIS 0.003 0.001 HIS C 547 Details of bonding type rmsd covalent geometry : bond 0.00223 (17100) covalent geometry : angle 0.53314 (23223) hydrogen bonds : bond 0.02955 ( 516) hydrogen bonds : angle 4.84427 ( 1347) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 53 HIS cc_start: 0.8192 (m-70) cc_final: 0.7694 (m170) REVERT: A 836 TRP cc_start: 0.8025 (m100) cc_final: 0.7730 (m100) REVERT: A 898 GLN cc_start: 0.8836 (pp30) cc_final: 0.8480 (pp30) REVERT: A 1084 SER cc_start: 0.8746 (m) cc_final: 0.8385 (t) REVERT: A 1088 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8603 (mp) REVERT: A 1105 LYS cc_start: 0.8036 (mttp) cc_final: 0.7722 (mmtm) REVERT: B 1020 ASP cc_start: 0.8715 (t0) cc_final: 0.8147 (m-30) REVERT: C 250 ASP cc_start: 0.7980 (t0) cc_final: 0.7644 (t0) REVERT: C 595 MET cc_start: 0.8175 (ttp) cc_final: 0.7916 (ttp) REVERT: C 660 TYR cc_start: 0.8684 (m-80) cc_final: 0.8409 (m-10) outliers start: 39 outliers final: 27 residues processed: 154 average time/residue: 0.1302 time to fit residues: 31.5422 Evaluate side-chains 147 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 549 CYS Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 865 HIS Chi-restraints excluded: chain A residue 890 GLN Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 1025 LYS Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1082 ILE Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1089 GLN Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain B residue 1009 VAL Chi-restraints excluded: chain B residue 1054 VAL Chi-restraints excluded: chain B residue 1097 ASN Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 623 MET Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 810 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 60 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 169 optimal weight: 7.9990 chunk 199 optimal weight: 5.9990 chunk 173 optimal weight: 7.9990 chunk 154 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 119 optimal weight: 0.2980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 GLN ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.084091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.067202 restraints weight = 42207.101| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.08 r_work: 0.3024 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17100 Z= 0.123 Angle : 0.546 15.580 23223 Z= 0.277 Chirality : 0.043 0.196 2468 Planarity : 0.004 0.054 3007 Dihedral : 4.482 30.961 2236 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.92 % Allowed : 14.71 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.19), residues: 2037 helix: 0.43 (0.30), residues: 318 sheet: -0.49 (0.21), residues: 642 loop : -1.00 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 95 TYR 0.016 0.001 TYR B1046 PHE 0.012 0.001 PHE C 688 TRP 0.007 0.001 TRP C 209 HIS 0.004 0.001 HIS D 561 Details of bonding type rmsd covalent geometry : bond 0.00287 (17100) covalent geometry : angle 0.54575 (23223) hydrogen bonds : bond 0.03098 ( 516) hydrogen bonds : angle 4.85055 ( 1347) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 53 HIS cc_start: 0.8093 (m-70) cc_final: 0.7653 (m170) REVERT: A 836 TRP cc_start: 0.8019 (m100) cc_final: 0.7755 (m100) REVERT: A 898 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8528 (pp30) REVERT: A 1084 SER cc_start: 0.8758 (m) cc_final: 0.8401 (t) REVERT: A 1088 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8625 (mp) REVERT: A 1089 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8297 (mt0) REVERT: A 1105 LYS cc_start: 0.8102 (mttp) cc_final: 0.7793 (mmtm) REVERT: B 1020 ASP cc_start: 0.8713 (t0) cc_final: 0.8125 (m-30) REVERT: C 250 ASP cc_start: 0.7996 (t0) cc_final: 0.7660 (t0) REVERT: C 595 MET cc_start: 0.8204 (ttp) cc_final: 0.7970 (ttp) outliers start: 35 outliers final: 28 residues processed: 146 average time/residue: 0.1381 time to fit residues: 30.9806 Evaluate side-chains 148 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 549 CYS Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 860 MET Chi-restraints excluded: chain A residue 865 HIS Chi-restraints excluded: chain A residue 890 GLN Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 898 GLN Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 1025 LYS Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1082 ILE Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1089 GLN Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain B residue 1009 VAL Chi-restraints excluded: chain B residue 1013 CYS Chi-restraints excluded: chain B residue 1054 VAL Chi-restraints excluded: chain B residue 1097 ASN Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 623 MET Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 810 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 190 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 148 optimal weight: 0.0030 chunk 178 optimal weight: 7.9990 chunk 174 optimal weight: 0.9990 chunk 192 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 GLN A 929 GLN ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.084345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.067176 restraints weight = 42543.002| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.13 r_work: 0.3025 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17100 Z= 0.115 Angle : 0.545 15.720 23223 Z= 0.276 Chirality : 0.043 0.195 2468 Planarity : 0.004 0.057 3007 Dihedral : 4.475 31.036 2236 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.09 % Allowed : 14.87 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.19), residues: 2037 helix: 0.48 (0.30), residues: 318 sheet: -0.43 (0.21), residues: 641 loop : -0.98 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 95 TYR 0.016 0.001 TYR B1046 PHE 0.012 0.001 PHE C 688 TRP 0.007 0.001 TRP C 209 HIS 0.009 0.001 HIS A 899 Details of bonding type rmsd covalent geometry : bond 0.00268 (17100) covalent geometry : angle 0.54520 (23223) hydrogen bonds : bond 0.03046 ( 516) hydrogen bonds : angle 4.82713 ( 1347) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 53 HIS cc_start: 0.8083 (m-70) cc_final: 0.7640 (m170) REVERT: A 836 TRP cc_start: 0.8017 (m100) cc_final: 0.7765 (m100) REVERT: A 898 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8586 (pp30) REVERT: A 1084 SER cc_start: 0.8754 (m) cc_final: 0.8401 (t) REVERT: A 1088 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8636 (mp) REVERT: A 1089 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8292 (mt0) REVERT: A 1105 LYS cc_start: 0.8119 (mttp) cc_final: 0.7820 (mmtm) REVERT: B 1020 ASP cc_start: 0.8713 (t0) cc_final: 0.8125 (m-30) REVERT: C 250 ASP cc_start: 0.7992 (t0) cc_final: 0.7658 (t0) REVERT: C 547 HIS cc_start: 0.9078 (OUTLIER) cc_final: 0.8273 (m-70) REVERT: C 595 MET cc_start: 0.8231 (ttp) cc_final: 0.8007 (ttp) outliers start: 38 outliers final: 29 residues processed: 147 average time/residue: 0.1324 time to fit residues: 29.8361 Evaluate side-chains 152 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 549 CYS Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 860 MET Chi-restraints excluded: chain A residue 865 HIS Chi-restraints excluded: chain A residue 890 GLN Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 898 GLN Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 1025 LYS Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1082 ILE Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1089 GLN Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain B residue 1009 VAL Chi-restraints excluded: chain B residue 1013 CYS Chi-restraints excluded: chain B residue 1050 SER Chi-restraints excluded: chain B residue 1054 VAL Chi-restraints excluded: chain B residue 1097 ASN Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 547 HIS Chi-restraints excluded: chain C residue 623 MET Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 810 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 18 optimal weight: 0.0970 chunk 26 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.084861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.068005 restraints weight = 42021.636| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.09 r_work: 0.3042 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17100 Z= 0.099 Angle : 0.546 15.885 23223 Z= 0.276 Chirality : 0.043 0.196 2468 Planarity : 0.004 0.056 3007 Dihedral : 4.420 31.150 2236 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.87 % Allowed : 15.15 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.19), residues: 2037 helix: 0.52 (0.30), residues: 324 sheet: -0.40 (0.21), residues: 656 loop : -1.01 (0.19), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 95 TYR 0.013 0.001 TYR B1046 PHE 0.011 0.001 PHE C 688 TRP 0.007 0.001 TRP C 209 HIS 0.009 0.001 HIS A 899 Details of bonding type rmsd covalent geometry : bond 0.00227 (17100) covalent geometry : angle 0.54611 (23223) hydrogen bonds : bond 0.02934 ( 516) hydrogen bonds : angle 4.77286 ( 1347) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4074 Ramachandran restraints generated. 2037 Oldfield, 0 Emsley, 2037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 53 HIS cc_start: 0.8076 (m-70) cc_final: 0.7630 (m170) REVERT: A 836 TRP cc_start: 0.8008 (m100) cc_final: 0.7765 (m100) REVERT: A 898 GLN cc_start: 0.8854 (pp30) cc_final: 0.8536 (pp30) REVERT: A 1084 SER cc_start: 0.8790 (m) cc_final: 0.8456 (t) REVERT: A 1088 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8621 (mp) REVERT: A 1089 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8280 (mt0) REVERT: A 1105 LYS cc_start: 0.8058 (mttp) cc_final: 0.7769 (mmtm) REVERT: B 1020 ASP cc_start: 0.8709 (t0) cc_final: 0.8134 (m-30) REVERT: C 250 ASP cc_start: 0.7984 (t0) cc_final: 0.7645 (t0) REVERT: C 557 MET cc_start: 0.8254 (ptp) cc_final: 0.7897 (ptp) outliers start: 34 outliers final: 30 residues processed: 145 average time/residue: 0.1335 time to fit residues: 30.0184 Evaluate side-chains 152 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 549 CYS Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain A residue 846 VAL Chi-restraints excluded: chain A residue 860 MET Chi-restraints excluded: chain A residue 865 HIS Chi-restraints excluded: chain A residue 890 GLN Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 1025 LYS Chi-restraints excluded: chain A residue 1077 ILE Chi-restraints excluded: chain A residue 1081 ASN Chi-restraints excluded: chain A residue 1082 ILE Chi-restraints excluded: chain A residue 1088 LEU Chi-restraints excluded: chain A residue 1089 GLN Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain B residue 1009 VAL Chi-restraints excluded: chain B residue 1013 CYS Chi-restraints excluded: chain B residue 1050 SER Chi-restraints excluded: chain B residue 1054 VAL Chi-restraints excluded: chain B residue 1097 ASN Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 325 HIS Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 623 MET Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 810 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 1 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 chunk 46 optimal weight: 0.0970 chunk 97 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 394 GLN ** D 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 929 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.084070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.067234 restraints weight = 42012.313| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.07 r_work: 0.3026 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17100 Z= 0.126 Angle : 0.558 15.454 23223 Z= 0.281 Chirality : 0.043 0.197 2468 Planarity : 0.004 0.057 3007 Dihedral : 4.459 30.817 2236 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.03 % Allowed : 14.98 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.19), residues: 2037 helix: 0.52 (0.30), residues: 324 sheet: -0.43 (0.21), residues: 661 loop : -0.99 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 95 TYR 0.016 0.001 TYR B1046 PHE 0.012 0.001 PHE C 688 TRP 0.006 0.001 TRP C 209 HIS 0.004 0.001 HIS C 741 Details of bonding type rmsd covalent geometry : bond 0.00296 (17100) covalent geometry : angle 0.55826 (23223) hydrogen bonds : bond 0.03070 ( 516) hydrogen bonds : angle 4.79676 ( 1347) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3281.04 seconds wall clock time: 57 minutes 23.52 seconds (3443.52 seconds total)