Starting phenix.real_space_refine on Thu Sep 18 18:53:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9are_43779/09_2025/9are_43779.cif Found real_map, /net/cci-nas-00/data/ceres_data/9are_43779/09_2025/9are_43779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9are_43779/09_2025/9are_43779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9are_43779/09_2025/9are_43779.map" model { file = "/net/cci-nas-00/data/ceres_data/9are_43779/09_2025/9are_43779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9are_43779/09_2025/9are_43779.cif" } resolution = 3.72 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= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 174 atoms to isotropic. 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 80 5.16 5 C 12190 2.51 5 N 3414 2.21 5 O 3538 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19222 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 4880 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 409} Link IDs: {'PTRANS': 34, 'TRANS': 760} Chain breaks: 2 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1458 Unresolved non-hydrogen angles: 1832 Unresolved non-hydrogen dihedrals: 1184 Unresolved non-hydrogen chiralities: 111 Planarities with less than four sites: {'ASN:plan1': 29, 'ARG:plan': 36, 'HIS:plan': 13, 'GLU:plan': 46, 'GLN:plan1': 25, 'PHE:plan': 9, 'ASP:plan': 29, 'TYR:plan': 11, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 843 Chain: "B" Number of atoms: 4716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 4716 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 434} Link IDs: {'PTRANS': 29, 'TRANS': 759} Chain breaks: 2 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1590 Unresolved non-hydrogen angles: 2028 Unresolved non-hydrogen dihedrals: 1331 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'ASP:plan': 45, 'GLU:plan': 45, 'HIS:plan': 9, 'PHE:plan': 19, 'ARG:plan': 19, 'ASN:plan1': 24, 'GLN:plan1': 22, 'TYR:plan': 20, 'TRP:plan': 7} Unresolved non-hydrogen planarities: 932 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Restraints were copied for chains: C, D Time building chain proxies: 7.33, per 1000 atoms: 0.38 Number of scatterers: 19222 At special positions: 0 Unit cell: (150.675, 133.455, 181.671, 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 80 16.00 O 3538 8.00 N 3414 7.00 C 12190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.02 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.02 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " distance=2.03 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: 1.66 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5920 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 28 sheets defined 44.2% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.616A pdb=" N GLU A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 103 through 112 removed outlier: 4.069A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 158 removed outlier: 3.876A pdb=" N SER A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 187 removed outlier: 4.011A pdb=" N ARG A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 Processing helix chain 'A' and resid 224 through 238 removed outlier: 3.653A pdb=" N ALA A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 256 through 261 removed outlier: 4.064A pdb=" N LEU A 259 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 296 removed outlier: 3.804A pdb=" N ILE A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 327 Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 527 removed outlier: 4.125A pdb=" N TYR A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 583 removed outlier: 3.622A pdb=" N VAL A 570 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N HIS A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 616 removed outlier: 3.845A pdb=" N LEU A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 655 removed outlier: 3.617A pdb=" N GLY A 638 " --> pdb=" O MET A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 694 Processing helix chain 'A' and resid 696 through 698 No H-bonds generated for 'chain 'A' and resid 696 through 698' Processing helix chain 'A' and resid 699 through 707 Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 733 through 743 Processing helix chain 'A' and resid 766 through 780 removed outlier: 4.097A pdb=" N SER A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU A 774 " --> pdb=" O GLN A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'A' and resid 812 through 822 Processing helix chain 'A' and resid 822 through 840 removed outlier: 3.929A pdb=" N ALA A 826 " --> pdb=" O GLY A 822 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE A 829 " --> pdb=" O VAL A 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 56 removed outlier: 3.531A pdb=" N ASP B 52 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 53 " --> pdb=" O ALA B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 removed outlier: 4.015A pdb=" N ARG B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 120 removed outlier: 4.320A pdb=" N ALA B 109 " --> pdb=" O GLN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 Processing helix chain 'B' and resid 176 through 192 removed outlier: 3.888A pdb=" N ASN B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 221 removed outlier: 3.642A pdb=" N LYS B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 288 through 311 Processing helix chain 'B' and resid 325 through 330 removed outlier: 3.989A pdb=" N ARG B 328 " --> pdb=" O HIS B 325 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B 329 " --> pdb=" O GLU B 326 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR B 330 " --> pdb=" O LYS B 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 325 through 330' Processing helix chain 'B' and resid 332 through 339 removed outlier: 3.621A pdb=" N ASN B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 473 removed outlier: 3.826A pdb=" N SER B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 473 " --> pdb=" O SER B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 516 through 523 Processing helix chain 'B' and resid 548 through 552 Processing helix chain 'B' and resid 555 through 581 Processing helix chain 'B' and resid 601 through 615 removed outlier: 3.570A pdb=" N VAL B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 646 Processing helix chain 'B' and resid 649 through 654 Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 689 through 699 removed outlier: 3.557A pdb=" N ASN B 698 " --> pdb=" O ASN B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 707 Processing helix chain 'B' and resid 713 through 724 Processing helix chain 'B' and resid 733 through 742 Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 771 through 787 removed outlier: 4.437A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.813A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 844 removed outlier: 4.053A pdb=" N MET B 818 " --> pdb=" O ASP B 814 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 821 " --> pdb=" O ASN B 817 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N MET B 824 " --> pdb=" O GLY B 820 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 825 " --> pdb=" O VAL B 821 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP B 844 " --> pdb=" O HIS B 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 50 removed outlier: 3.616A pdb=" N GLU C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 86 Processing helix chain 'C' and resid 103 through 112 removed outlier: 4.068A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 158 removed outlier: 3.876A pdb=" N SER C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 187 removed outlier: 4.012A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 212 Processing helix chain 'C' and resid 224 through 238 removed outlier: 3.653A pdb=" N ALA C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 256 through 261 removed outlier: 4.063A pdb=" N LEU C 259 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 296 removed outlier: 3.804A pdb=" N ILE C 281 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 327 Processing helix chain 'C' and resid 458 through 471 Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 520 through 527 removed outlier: 4.125A pdb=" N TYR C 526 " --> pdb=" O GLU C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 583 removed outlier: 3.622A pdb=" N VAL C 570 " --> pdb=" O VAL C 566 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N HIS C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 616 removed outlier: 3.845A pdb=" N LEU C 614 " --> pdb=" O SER C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 655 removed outlier: 3.616A pdb=" N GLY C 638 " --> pdb=" O MET C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 695 Processing helix chain 'C' and resid 696 through 698 No H-bonds generated for 'chain 'C' and resid 696 through 698' Processing helix chain 'C' and resid 699 through 707 Processing helix chain 'C' and resid 713 through 723 Processing helix chain 'C' and resid 733 through 743 Processing helix chain 'C' and resid 766 through 780 removed outlier: 4.097A pdb=" N SER C 773 " --> pdb=" O LYS C 769 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU C 774 " --> pdb=" O GLN C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'C' and resid 812 through 822 Processing helix chain 'C' and resid 822 through 840 removed outlier: 3.929A pdb=" N ALA C 826 " --> pdb=" O GLY C 822 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE C 829 " --> pdb=" O VAL C 825 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 56 removed outlier: 3.531A pdb=" N ASP D 52 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA D 53 " --> pdb=" O ALA D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 92 removed outlier: 4.015A pdb=" N ARG D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 120 removed outlier: 4.320A pdb=" N ALA D 109 " --> pdb=" O GLN D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 164 Processing helix chain 'D' and resid 176 through 192 removed outlier: 3.888A pdb=" N ASN D 192 " --> pdb=" O SER D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 221 removed outlier: 3.642A pdb=" N LYS D 221 " --> pdb=" O GLN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 288 through 311 Processing helix chain 'D' and resid 325 through 330 removed outlier: 3.989A pdb=" N ARG D 328 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE D 329 " --> pdb=" O GLU D 326 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR D 330 " --> pdb=" O LYS D 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 325 through 330' Processing helix chain 'D' and resid 332 through 339 removed outlier: 3.622A pdb=" N ASN D 336 " --> pdb=" O SER D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 473 removed outlier: 3.826A pdb=" N SER D 471 " --> pdb=" O LYS D 467 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS D 473 " --> pdb=" O SER D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 503 Processing helix chain 'D' and resid 516 through 523 Processing helix chain 'D' and resid 548 through 552 Processing helix chain 'D' and resid 555 through 581 Processing helix chain 'D' and resid 601 through 615 removed outlier: 3.569A pdb=" N VAL D 613 " --> pdb=" O LEU D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 646 Processing helix chain 'D' and resid 649 through 654 Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 689 through 699 removed outlier: 3.557A pdb=" N ASN D 698 " --> pdb=" O ASN D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 707 Processing helix chain 'D' and resid 713 through 724 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 752 through 754 No H-bonds generated for 'chain 'D' and resid 752 through 754' Processing helix chain 'D' and resid 771 through 787 removed outlier: 4.437A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 797 removed outlier: 3.813A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 844 removed outlier: 4.053A pdb=" N MET D 818 " --> pdb=" O ASP D 814 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL D 821 " --> pdb=" O ASN D 817 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N MET D 824 " --> pdb=" O GLY D 820 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU D 825 " --> pdb=" O VAL D 821 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP D 844 " --> pdb=" O HIS D 840 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 65 removed outlier: 3.767A pdb=" N VAL A 65 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 removed outlier: 7.103A pdb=" N ILE A 163 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N LEU A 195 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N SER A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 166 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A 219 " --> pdb=" O VAL A 246 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 268 removed outlier: 3.576A pdb=" N MET A 354 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 478 removed outlier: 7.003A pdb=" N LEU A 398 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N HIS A 477 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 409 through 412 removed outlier: 3.556A pdb=" N TYR A 456 " --> pdb=" O TYR A 410 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 528 through 529 removed outlier: 3.642A pdb=" N GLU A 528 " --> pdb=" O MET A 762 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 681 through 682 removed outlier: 7.019A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU A 538 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLU A 751 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 67 through 73 removed outlier: 6.750A pdb=" N GLY B 36 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N VAL B 97 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA B 38 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N PHE B 99 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE B 40 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ASP B 101 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL B 42 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N LEU B 124 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE B 126 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N PHE B 99 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY B 128 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASP B 101 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE B 144 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 198 through 203 removed outlier: 8.124A pdb=" N PHE B 169 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 9.668A pdb=" N LEU B 203 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE B 168 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N LEU B 229 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER B 170 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N TYR B 231 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL B 172 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL B 258 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 10.005A pdb=" N TYR B 282 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER B 279 " --> pdb=" O ILE B 365 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU B 366 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ARG B 375 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 476 through 480 removed outlier: 3.552A pdb=" N ASP B 524 " --> pdb=" O ILE B 766 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 418 through 420 removed outlier: 3.512A pdb=" N VAL B 434 " --> pdb=" O CYS B 457 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 489 through 490 removed outlier: 4.078A pdb=" N ILE B 490 " --> pdb=" O THR B 493 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 729 through 732 removed outlier: 3.934A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 535 " --> pdb=" O TYR B 731 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 729 through 732 removed outlier: 3.934A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 535 " --> pdb=" O TYR B 731 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N THR B 532 " --> pdb=" O SER B 759 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER B 759 " --> pdb=" O THR B 532 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 62 through 65 removed outlier: 3.767A pdb=" N VAL C 65 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 193 through 197 removed outlier: 7.103A pdb=" N ILE C 163 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N LEU C 195 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE C 164 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N SER C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU C 166 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE C 219 " --> pdb=" O VAL C 246 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 267 through 268 removed outlier: 3.576A pdb=" N MET C 354 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 473 through 478 removed outlier: 7.003A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 409 through 412 removed outlier: 3.556A pdb=" N TYR C 456 " --> pdb=" O TYR C 410 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 528 through 529 removed outlier: 3.642A pdb=" N GLU C 528 " --> pdb=" O MET C 762 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 681 through 682 removed outlier: 7.019A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 9.512A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU C 538 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLU C 751 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 67 through 73 removed outlier: 6.751A pdb=" N GLY D 36 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N VAL D 97 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA D 38 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N PHE D 99 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE D 40 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ASP D 101 " --> pdb=" O ILE D 40 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL D 42 " --> pdb=" O ASP D 101 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N LEU D 124 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE D 126 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N PHE D 99 " --> pdb=" O ILE D 126 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY D 128 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASP D 101 " --> pdb=" O GLY D 128 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE D 144 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 198 through 203 removed outlier: 8.124A pdb=" N PHE D 169 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 9.668A pdb=" N LEU D 203 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE D 168 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N LEU D 229 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER D 170 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N TYR D 231 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL D 172 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL D 258 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N TYR D 282 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER D 279 " --> pdb=" O ILE D 365 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU D 366 " --> pdb=" O ARG D 375 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ARG D 375 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 476 through 480 removed outlier: 3.551A pdb=" N ASP D 524 " --> pdb=" O ILE D 766 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 418 through 420 removed outlier: 3.511A pdb=" N VAL D 434 " --> pdb=" O CYS D 457 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 489 through 490 removed outlier: 4.078A pdb=" N ILE D 490 " --> pdb=" O THR D 493 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 729 through 732 removed outlier: 3.934A pdb=" N TYR D 731 " --> pdb=" O SER D 535 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER D 535 " --> pdb=" O TYR D 731 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 729 through 732 removed outlier: 3.934A pdb=" N TYR D 731 " --> pdb=" O SER D 535 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER D 535 " --> pdb=" O TYR D 731 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N THR D 532 " --> pdb=" O SER D 759 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER D 759 " --> pdb=" O THR D 532 " (cutoff:3.500A) 1059 hydrogen bonds defined for protein. 3075 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: 3.87 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.21: 56 1.21 - 1.36: 6669 1.36 - 1.52: 5633 1.52 - 1.67: 7032 1.67 - 1.82: 132 Bond restraints: 19522 Sorted by residual: bond pdb=" C LYS A 534 " pdb=" O LYS A 534 " ideal model delta sigma weight residual 1.235 1.060 0.175 1.26e-02 6.30e+03 1.93e+02 bond pdb=" C LYS C 534 " pdb=" O LYS C 534 " ideal model delta sigma weight residual 1.235 1.061 0.175 1.26e-02 6.30e+03 1.92e+02 bond pdb=" C PRO C 532 " pdb=" O PRO C 532 " ideal model delta sigma weight residual 1.233 1.076 0.157 1.24e-02 6.50e+03 1.61e+02 bond pdb=" C PRO A 532 " pdb=" O PRO A 532 " ideal model delta sigma weight residual 1.233 1.076 0.157 1.24e-02 6.50e+03 1.60e+02 bond pdb=" C PHE A 533 " pdb=" O PHE A 533 " ideal model delta sigma weight residual 1.236 1.066 0.170 1.39e-02 5.18e+03 1.50e+02 ... (remaining 19517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.52: 26836 6.52 - 13.03: 74 13.03 - 19.55: 2 19.55 - 26.07: 0 26.07 - 32.58: 2 Bond angle restraints: 26914 Sorted by residual: angle pdb=" CB MET C 762 " pdb=" CG MET C 762 " pdb=" SD MET C 762 " ideal model delta sigma weight residual 112.70 80.12 32.58 3.00e+00 1.11e-01 1.18e+02 angle pdb=" CB MET A 762 " pdb=" CG MET A 762 " pdb=" SD MET A 762 " ideal model delta sigma weight residual 112.70 80.13 32.57 3.00e+00 1.11e-01 1.18e+02 angle pdb=" C HIS A 780 " pdb=" CA HIS A 780 " pdb=" CB HIS A 780 " ideal model delta sigma weight residual 109.29 89.83 19.46 1.82e+00 3.02e-01 1.14e+02 angle pdb=" C HIS C 780 " pdb=" CA HIS C 780 " pdb=" CB HIS C 780 " ideal model delta sigma weight residual 109.29 89.85 19.44 1.82e+00 3.02e-01 1.14e+02 angle pdb=" CA PHE A 533 " pdb=" C PHE A 533 " pdb=" O PHE A 533 " ideal model delta sigma weight residual 119.32 108.56 10.76 1.19e+00 7.06e-01 8.17e+01 ... (remaining 26909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 10590 17.64 - 35.28: 502 35.28 - 52.92: 132 52.92 - 70.56: 16 70.56 - 88.20: 6 Dihedral angle restraints: 11246 sinusoidal: 2120 harmonic: 9126 Sorted by residual: dihedral pdb=" CB CYS A 744 " pdb=" SG CYS A 744 " pdb=" SG CYS A 798 " pdb=" CB CYS A 798 " ideal model delta sinusoidal sigma weight residual 93.00 -178.80 -88.20 1 1.00e+01 1.00e-02 9.30e+01 dihedral pdb=" CB CYS C 744 " pdb=" SG CYS C 744 " pdb=" SG CYS C 798 " pdb=" CB CYS C 798 " ideal model delta sinusoidal sigma weight residual 93.00 -178.83 -88.17 1 1.00e+01 1.00e-02 9.29e+01 dihedral pdb=" C HIS A 780 " pdb=" N HIS A 780 " pdb=" CA HIS A 780 " pdb=" CB HIS A 780 " ideal model delta harmonic sigma weight residual -122.60 -98.64 -23.96 0 2.50e+00 1.60e-01 9.18e+01 ... (remaining 11243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.206: 3362 0.206 - 0.412: 36 0.412 - 0.619: 16 0.619 - 0.825: 0 0.825 - 1.031: 2 Chirality restraints: 3416 Sorted by residual: chirality pdb=" CA SER B 617 " pdb=" N SER B 617 " pdb=" C SER B 617 " pdb=" CB SER B 617 " both_signs ideal model delta sigma weight residual False 2.51 1.48 1.03 2.00e-01 2.50e+01 2.66e+01 chirality pdb=" CA SER D 617 " pdb=" N SER D 617 " pdb=" C SER D 617 " pdb=" CB SER D 617 " both_signs ideal model delta sigma weight residual False 2.51 1.48 1.03 2.00e-01 2.50e+01 2.66e+01 chirality pdb=" CA LEU A 651 " pdb=" N LEU A 651 " pdb=" C LEU A 651 " pdb=" CB LEU A 651 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.80e+00 ... (remaining 3413 not shown) Planarity restraints: 3546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 609 " 0.034 2.00e-02 2.50e+03 6.83e-02 4.66e+01 pdb=" C LEU B 609 " -0.118 2.00e-02 2.50e+03 pdb=" O LEU B 609 " 0.044 2.00e-02 2.50e+03 pdb=" N TRP B 610 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 609 " -0.034 2.00e-02 2.50e+03 6.80e-02 4.63e+01 pdb=" C LEU D 609 " 0.118 2.00e-02 2.50e+03 pdb=" O LEU D 609 " -0.044 2.00e-02 2.50e+03 pdb=" N TRP D 610 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 533 " 0.025 2.00e-02 2.50e+03 5.47e-02 2.99e+01 pdb=" C PHE A 533 " -0.095 2.00e-02 2.50e+03 pdb=" O PHE A 533 " 0.036 2.00e-02 2.50e+03 pdb=" N LYS A 534 " 0.034 2.00e-02 2.50e+03 ... (remaining 3543 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 367 2.68 - 3.23: 18024 3.23 - 3.79: 27037 3.79 - 4.34: 31120 4.34 - 4.90: 53219 Nonbonded interactions: 129767 Sorted by model distance: nonbonded pdb=" O MET B 818 " pdb=" CD1 PHE B 822 " model vdw 2.124 3.340 nonbonded pdb=" O MET D 818 " pdb=" CD1 PHE D 822 " model vdw 2.125 3.340 nonbonded pdb=" O SER B 617 " pdb=" OG SER B 617 " model vdw 2.232 3.040 nonbonded pdb=" O SER D 617 " pdb=" OG SER D 617 " model vdw 2.232 3.040 nonbonded pdb=" O THR C 35 " pdb=" N HIS C 38 " model vdw 2.283 3.120 ... (remaining 129762 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 6.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.470 Find NCS groups from input model: 0.160 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: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6303 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 : 0.007 0.175 19534 Z= 0.492 Angle : 0.983 32.582 26938 Z= 0.640 Chirality : 0.068 1.031 3416 Planarity : 0.006 0.068 3546 Dihedral : 11.574 74.183 5290 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.80 % Favored : 95.07 % Rotamer: Outliers : 5.24 % Allowed : 6.27 % Favored : 88.48 % Cbeta Deviations : 1.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.47 (0.13), residues: 3144 helix: -0.41 (0.13), residues: 1312 sheet: -2.02 (0.22), residues: 432 loop : -2.74 (0.14), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 722 TYR 0.026 0.001 TYR C 692 PHE 0.058 0.003 PHE D 460 TRP 0.021 0.001 TRP B 610 HIS 0.012 0.002 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00722 (19522) covalent geometry : angle 0.98171 (26914) SS BOND : bond 0.00454 ( 12) SS BOND : angle 2.02788 ( 24) hydrogen bonds : bond 0.17908 ( 1055) hydrogen bonds : angle 6.18503 ( 3075) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 315 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.7155 (mtp) cc_final: 0.6735 (ttm) REVERT: A 641 MET cc_start: 0.8762 (tmt) cc_final: 0.8422 (tmt) REVERT: A 651 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8869 (tp) REVERT: A 693 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.7521 (t80) REVERT: B 391 TRP cc_start: 0.6977 (OUTLIER) cc_final: 0.6223 (t60) REVERT: B 554 PHE cc_start: 0.6370 (OUTLIER) cc_final: 0.5556 (m-10) REVERT: B 630 ILE cc_start: 0.8291 (mm) cc_final: 0.8026 (mt) REVERT: B 643 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9092 (tt) REVERT: C 501 MET cc_start: 0.7269 (mtp) cc_final: 0.6747 (ttm) REVERT: C 536 GLN cc_start: 0.7924 (pp30) cc_final: 0.7711 (pp30) REVERT: C 641 MET cc_start: 0.8838 (tmt) cc_final: 0.8477 (tmt) REVERT: C 651 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8927 (tp) REVERT: C 693 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.7444 (t80) REVERT: D 391 TRP cc_start: 0.7153 (OUTLIER) cc_final: 0.5902 (t60) REVERT: D 630 ILE cc_start: 0.8324 (mm) cc_final: 0.8051 (mt) REVERT: D 643 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9040 (tt) outliers start: 56 outliers final: 37 residues processed: 365 average time/residue: 0.1027 time to fit residues: 63.9496 Evaluate side-chains 285 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 239 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 532 PRO Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 608 TRP Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 692 TYR Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain B residue 391 TRP Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 550 PHE Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 532 PRO Chi-restraints excluded: chain C residue 533 PHE Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 692 TYR Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain D residue 391 TRP Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 507 TYR Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 643 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 30.0000 chunk 298 optimal weight: 0.0470 overall best weight: 1.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 HIS A 771 GLN C 477 HIS C 771 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.203329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.175745 restraints weight = 30593.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.172213 restraints weight = 45499.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.169884 restraints weight = 45194.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.169564 restraints weight = 46655.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.168561 restraints weight = 39528.423| |-----------------------------------------------------------------------------| r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 19534 Z= 0.194 Angle : 0.592 7.489 26938 Z= 0.326 Chirality : 0.045 0.226 3416 Planarity : 0.004 0.073 3546 Dihedral : 6.498 59.190 3327 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.66 % Favored : 94.27 % Rotamer: Outliers : 6.37 % Allowed : 16.29 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.15), residues: 3144 helix: 0.84 (0.14), residues: 1356 sheet: -1.38 (0.26), residues: 326 loop : -2.36 (0.15), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 763 TYR 0.027 0.002 TYR B 479 PHE 0.034 0.002 PHE C 533 TRP 0.013 0.002 TRP C 636 HIS 0.005 0.001 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00461 (19522) covalent geometry : angle 0.59017 (26914) SS BOND : bond 0.00832 ( 12) SS BOND : angle 1.51793 ( 24) hydrogen bonds : bond 0.04772 ( 1055) hydrogen bonds : angle 4.71215 ( 3075) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 239 time to evaluate : 0.481 Fit side-chains REVERT: A 501 MET cc_start: 0.7617 (mtp) cc_final: 0.7222 (ttm) REVERT: A 565 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7656 (tp) REVERT: B 554 PHE cc_start: 0.6703 (OUTLIER) cc_final: 0.5853 (m-10) REVERT: B 643 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8286 (mt) REVERT: C 501 MET cc_start: 0.7649 (mtp) cc_final: 0.7192 (ttm) REVERT: D 554 PHE cc_start: 0.6937 (OUTLIER) cc_final: 0.6460 (m-10) REVERT: D 643 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8555 (tt) outliers start: 68 outliers final: 44 residues processed: 291 average time/residue: 0.0939 time to fit residues: 48.1281 Evaluate side-chains 278 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 229 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 1001 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 48 optimal weight: 0.0870 chunk 257 optimal weight: 1.9990 chunk 33 optimal weight: 50.0000 chunk 178 optimal weight: 0.3980 chunk 134 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 80 optimal weight: 20.0000 chunk 87 optimal weight: 0.0070 chunk 152 optimal weight: 5.9990 chunk 121 optimal weight: 0.0980 chunk 256 optimal weight: 40.0000 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.203685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.177826 restraints weight = 30691.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.174384 restraints weight = 42950.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.173644 restraints weight = 41025.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.172884 restraints weight = 39164.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.172123 restraints weight = 35291.765| |-----------------------------------------------------------------------------| r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 19534 Z= 0.101 Angle : 0.476 6.423 26938 Z= 0.259 Chirality : 0.042 0.171 3416 Planarity : 0.003 0.074 3546 Dihedral : 5.352 54.707 3272 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.36 % Favored : 95.58 % Rotamer: Outliers : 5.52 % Allowed : 20.04 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.15), residues: 3144 helix: 1.50 (0.15), residues: 1356 sheet: -1.45 (0.25), residues: 372 loop : -1.94 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 763 TYR 0.015 0.001 TYR B 479 PHE 0.037 0.001 PHE C 654 TRP 0.014 0.001 TRP C 636 HIS 0.004 0.001 HIS C 404 Details of bonding type rmsd covalent geometry : bond 0.00212 (19522) covalent geometry : angle 0.47488 (26914) SS BOND : bond 0.00113 ( 12) SS BOND : angle 1.09880 ( 24) hydrogen bonds : bond 0.03247 ( 1055) hydrogen bonds : angle 4.10407 ( 3075) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 247 time to evaluate : 1.176 Fit side-chains REVERT: A 824 ILE cc_start: 0.6072 (mp) cc_final: 0.5451 (tp) REVERT: B 391 TRP cc_start: 0.7028 (OUTLIER) cc_final: 0.6136 (t60) REVERT: B 554 PHE cc_start: 0.6806 (OUTLIER) cc_final: 0.5874 (m-10) REVERT: B 643 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8089 (mt) REVERT: B 666 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8718 (pp) REVERT: B 671 PHE cc_start: 0.7789 (OUTLIER) cc_final: 0.6443 (m-10) REVERT: B 834 ILE cc_start: 0.8779 (pt) cc_final: 0.8559 (mt) REVERT: D 391 TRP cc_start: 0.7230 (OUTLIER) cc_final: 0.5851 (t60) REVERT: D 554 PHE cc_start: 0.6892 (OUTLIER) cc_final: 0.6462 (m-10) REVERT: D 671 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.6420 (m-10) outliers start: 59 outliers final: 34 residues processed: 295 average time/residue: 0.0983 time to fit residues: 51.5162 Evaluate side-chains 273 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 231 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain B residue 391 TRP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain D residue 391 TRP Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 671 PHE Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 1001 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 61 optimal weight: 0.3980 chunk 244 optimal weight: 7.9990 chunk 97 optimal weight: 50.0000 chunk 69 optimal weight: 0.0370 chunk 42 optimal weight: 4.9990 chunk 267 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 83 optimal weight: 50.0000 chunk 289 optimal weight: 8.9990 chunk 31 optimal weight: 30.0000 chunk 34 optimal weight: 40.0000 overall best weight: 2.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 771 GLN C 771 GLN D 694 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.195607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.167746 restraints weight = 30812.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.164458 restraints weight = 44598.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.160700 restraints weight = 46634.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.159600 restraints weight = 43195.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.157689 restraints weight = 43448.696| |-----------------------------------------------------------------------------| r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 19534 Z= 0.255 Angle : 0.646 8.416 26938 Z= 0.353 Chirality : 0.047 0.213 3416 Planarity : 0.004 0.070 3546 Dihedral : 5.666 57.015 3270 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.01 % Favored : 93.89 % Rotamer: Outliers : 7.87 % Allowed : 21.82 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.15), residues: 3144 helix: 1.52 (0.15), residues: 1336 sheet: -1.00 (0.27), residues: 344 loop : -2.00 (0.15), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 763 TYR 0.037 0.002 TYR D 479 PHE 0.043 0.003 PHE C 533 TRP 0.017 0.002 TRP C 636 HIS 0.009 0.002 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00618 (19522) covalent geometry : angle 0.64594 (26914) SS BOND : bond 0.00354 ( 12) SS BOND : angle 1.00661 ( 24) hydrogen bonds : bond 0.05520 ( 1055) hydrogen bonds : angle 4.68977 ( 3075) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 230 time to evaluate : 0.597 Fit side-chains REVERT: A 565 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7827 (tp) REVERT: A 615 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8664 (mt) REVERT: B 391 TRP cc_start: 0.7188 (OUTLIER) cc_final: 0.6298 (t60) REVERT: B 554 PHE cc_start: 0.7039 (OUTLIER) cc_final: 0.6289 (m-10) REVERT: B 630 ILE cc_start: 0.8617 (mm) cc_final: 0.8397 (mt) REVERT: B 671 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7000 (m-10) REVERT: C 565 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7856 (tp) REVERT: C 615 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8648 (mt) REVERT: D 391 TRP cc_start: 0.7322 (OUTLIER) cc_final: 0.6007 (t60) REVERT: D 468 ILE cc_start: 0.8594 (mt) cc_final: 0.8374 (mt) REVERT: D 554 PHE cc_start: 0.7201 (OUTLIER) cc_final: 0.6628 (m-10) REVERT: D 671 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.6992 (m-10) outliers start: 84 outliers final: 52 residues processed: 295 average time/residue: 0.0896 time to fit residues: 46.9667 Evaluate side-chains 279 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 217 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 391 TRP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 391 TRP Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 671 PHE Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 751 ILE Chi-restraints excluded: chain B residue 1001 GLU Chi-restraints excluded: chain D residue 1001 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 289 optimal weight: 5.9990 chunk 0 optimal weight: 100.0000 chunk 250 optimal weight: 40.0000 chunk 15 optimal weight: 8.9990 chunk 150 optimal weight: 0.6980 chunk 225 optimal weight: 1.9990 chunk 224 optimal weight: 5.9990 chunk 280 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 3 optimal weight: 30.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.195394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.167405 restraints weight = 30753.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.165393 restraints weight = 44885.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.163075 restraints weight = 44688.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.161953 restraints weight = 43738.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.159515 restraints weight = 44178.400| |-----------------------------------------------------------------------------| r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 19534 Z= 0.237 Angle : 0.616 7.962 26938 Z= 0.336 Chirality : 0.046 0.177 3416 Planarity : 0.004 0.062 3546 Dihedral : 5.700 59.088 3270 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.27 % Favored : 93.67 % Rotamer: Outliers : 9.18 % Allowed : 23.60 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.15), residues: 3144 helix: 1.51 (0.15), residues: 1338 sheet: -1.07 (0.27), residues: 326 loop : -2.06 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 763 TYR 0.034 0.002 TYR D 479 PHE 0.037 0.003 PHE C 533 TRP 0.019 0.002 TRP C 636 HIS 0.007 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00579 (19522) covalent geometry : angle 0.61296 (26914) SS BOND : bond 0.00702 ( 12) SS BOND : angle 2.22420 ( 24) hydrogen bonds : bond 0.05124 ( 1055) hydrogen bonds : angle 4.54180 ( 3075) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 218 time to evaluate : 0.667 Fit side-chains REVERT: A 565 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7801 (tp) REVERT: A 615 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8628 (mt) REVERT: B 391 TRP cc_start: 0.7158 (OUTLIER) cc_final: 0.6233 (t60) REVERT: B 507 TYR cc_start: 0.7160 (OUTLIER) cc_final: 0.6565 (t80) REVERT: B 554 PHE cc_start: 0.7145 (OUTLIER) cc_final: 0.6469 (m-10) REVERT: B 630 ILE cc_start: 0.8594 (mm) cc_final: 0.8380 (mt) REVERT: B 671 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.6925 (m-10) REVERT: B 834 ILE cc_start: 0.8884 (pt) cc_final: 0.8509 (mt) REVERT: C 536 GLN cc_start: 0.8498 (pp30) cc_final: 0.8245 (pp30) REVERT: C 565 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7832 (tp) REVERT: C 615 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8626 (mt) REVERT: D 391 TRP cc_start: 0.7322 (OUTLIER) cc_final: 0.5942 (t60) REVERT: D 468 ILE cc_start: 0.8594 (mt) cc_final: 0.8353 (mt) REVERT: D 554 PHE cc_start: 0.7111 (OUTLIER) cc_final: 0.6647 (m-10) REVERT: D 671 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.6991 (m-10) REVERT: D 834 ILE cc_start: 0.8831 (pt) cc_final: 0.8559 (mt) outliers start: 98 outliers final: 63 residues processed: 296 average time/residue: 0.0924 time to fit residues: 48.2932 Evaluate side-chains 286 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 212 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 391 TRP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain D residue 391 TRP Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 521 GLU Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 671 PHE Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 751 ILE Chi-restraints excluded: chain D residue 1001 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 234 optimal weight: 7.9990 chunk 273 optimal weight: 1.9990 chunk 69 optimal weight: 0.0000 chunk 223 optimal weight: 3.9990 chunk 210 optimal weight: 0.6980 chunk 236 optimal weight: 50.0000 chunk 307 optimal weight: 0.8980 chunk 81 optimal weight: 40.0000 chunk 101 optimal weight: 7.9990 chunk 180 optimal weight: 40.0000 chunk 5 optimal weight: 50.0000 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.197267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.169362 restraints weight = 30692.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.166746 restraints weight = 44495.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.163606 restraints weight = 39250.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.163055 restraints weight = 39002.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.160627 restraints weight = 37648.343| |-----------------------------------------------------------------------------| r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19534 Z= 0.149 Angle : 0.535 8.721 26938 Z= 0.288 Chirality : 0.043 0.172 3416 Planarity : 0.003 0.060 3546 Dihedral : 5.196 58.854 3266 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.14 % Favored : 93.80 % Rotamer: Outliers : 8.43 % Allowed : 24.91 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.16), residues: 3144 helix: 1.73 (0.15), residues: 1338 sheet: -1.18 (0.26), residues: 350 loop : -1.94 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 763 TYR 0.026 0.001 TYR B 479 PHE 0.026 0.002 PHE C 533 TRP 0.018 0.001 TRP C 636 HIS 0.004 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00349 (19522) covalent geometry : angle 0.53410 (26914) SS BOND : bond 0.00181 ( 12) SS BOND : angle 1.07419 ( 24) hydrogen bonds : bond 0.04023 ( 1055) hydrogen bonds : angle 4.19377 ( 3075) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 211 time to evaluate : 0.735 Fit side-chains REVERT: A 478 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8509 (mp) REVERT: A 709 HIS cc_start: 0.8144 (OUTLIER) cc_final: 0.7544 (p90) REVERT: B 391 TRP cc_start: 0.7161 (OUTLIER) cc_final: 0.6230 (t60) REVERT: B 554 PHE cc_start: 0.7045 (OUTLIER) cc_final: 0.6291 (m-10) REVERT: B 671 PHE cc_start: 0.7918 (OUTLIER) cc_final: 0.6845 (m-10) REVERT: C 478 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8507 (mp) REVERT: C 709 HIS cc_start: 0.8178 (OUTLIER) cc_final: 0.7591 (p90) REVERT: D 391 TRP cc_start: 0.7305 (OUTLIER) cc_final: 0.5937 (t60) REVERT: D 468 ILE cc_start: 0.8533 (mt) cc_final: 0.8315 (mt) REVERT: D 554 PHE cc_start: 0.6970 (OUTLIER) cc_final: 0.6527 (m-10) REVERT: D 671 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.6854 (m-10) outliers start: 90 outliers final: 60 residues processed: 286 average time/residue: 0.0926 time to fit residues: 46.8490 Evaluate side-chains 270 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 200 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 391 TRP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 829 MET Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain D residue 391 TRP Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 671 PHE Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain B residue 1001 GLU Chi-restraints excluded: chain D residue 1001 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 39 optimal weight: 0.9990 chunk 238 optimal weight: 0.3980 chunk 219 optimal weight: 1.9990 chunk 258 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 276 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 214 optimal weight: 0.0870 chunk 259 optimal weight: 0.0060 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.199498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.172208 restraints weight = 30969.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.168160 restraints weight = 45799.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.165836 restraints weight = 44760.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.165319 restraints weight = 46457.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.163501 restraints weight = 41662.859| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19534 Z= 0.102 Angle : 0.497 8.839 26938 Z= 0.262 Chirality : 0.042 0.213 3416 Planarity : 0.003 0.053 3546 Dihedral : 4.771 56.593 3264 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.25 % Favored : 94.69 % Rotamer: Outliers : 6.93 % Allowed : 27.34 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.16), residues: 3144 helix: 1.89 (0.15), residues: 1346 sheet: -1.32 (0.25), residues: 396 loop : -1.70 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 523 TYR 0.029 0.001 TYR C 703 PHE 0.015 0.001 PHE A 654 TRP 0.018 0.001 TRP C 636 HIS 0.004 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00221 (19522) covalent geometry : angle 0.49538 (26914) SS BOND : bond 0.00127 ( 12) SS BOND : angle 1.52933 ( 24) hydrogen bonds : bond 0.03243 ( 1055) hydrogen bonds : angle 3.94711 ( 3075) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 212 time to evaluate : 0.781 Fit side-chains REVERT: B 391 TRP cc_start: 0.7140 (OUTLIER) cc_final: 0.6211 (t60) REVERT: B 554 PHE cc_start: 0.6998 (OUTLIER) cc_final: 0.6216 (m-10) REVERT: B 671 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.6801 (m-10) REVERT: D 391 TRP cc_start: 0.7328 (OUTLIER) cc_final: 0.5964 (t60) REVERT: D 554 PHE cc_start: 0.7096 (OUTLIER) cc_final: 0.6664 (m-10) REVERT: D 671 PHE cc_start: 0.7861 (OUTLIER) cc_final: 0.6728 (m-10) REVERT: B 1001 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6965 (tp30) outliers start: 74 outliers final: 50 residues processed: 278 average time/residue: 0.0959 time to fit residues: 47.0327 Evaluate side-chains 261 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 204 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain B residue 391 TRP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 829 MET Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain D residue 391 TRP Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 521 GLU Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 671 PHE Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain B residue 1001 GLU Chi-restraints excluded: chain D residue 1001 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 119 optimal weight: 0.0070 chunk 161 optimal weight: 50.0000 chunk 70 optimal weight: 4.9990 chunk 58 optimal weight: 0.0980 chunk 164 optimal weight: 9.9990 chunk 186 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 201 optimal weight: 1.9990 chunk 305 optimal weight: 4.9990 chunk 290 optimal weight: 10.0000 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.198328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.171509 restraints weight = 30836.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.167415 restraints weight = 42813.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.162943 restraints weight = 48236.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.162784 restraints weight = 49290.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.161357 restraints weight = 39710.492| |-----------------------------------------------------------------------------| r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19534 Z= 0.129 Angle : 0.530 9.459 26938 Z= 0.278 Chirality : 0.043 0.224 3416 Planarity : 0.003 0.050 3546 Dihedral : 4.651 58.260 3260 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.11 % Favored : 93.83 % Rotamer: Outliers : 6.84 % Allowed : 26.78 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.16), residues: 3144 helix: 1.96 (0.15), residues: 1344 sheet: -1.21 (0.26), residues: 388 loop : -1.67 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 763 TYR 0.030 0.001 TYR B 705 PHE 0.024 0.002 PHE C 533 TRP 0.016 0.001 TRP C 636 HIS 0.004 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00302 (19522) covalent geometry : angle 0.52776 (26914) SS BOND : bond 0.00166 ( 12) SS BOND : angle 1.54500 ( 24) hydrogen bonds : bond 0.03611 ( 1055) hydrogen bonds : angle 3.99804 ( 3075) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 202 time to evaluate : 0.729 Fit side-chains REVERT: A 478 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8507 (mp) REVERT: B 391 TRP cc_start: 0.7162 (OUTLIER) cc_final: 0.6228 (t60) REVERT: B 554 PHE cc_start: 0.6950 (OUTLIER) cc_final: 0.6218 (m-10) REVERT: B 671 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.6778 (m-10) REVERT: C 478 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8493 (mp) REVERT: D 391 TRP cc_start: 0.7324 (OUTLIER) cc_final: 0.6061 (t60) REVERT: D 554 PHE cc_start: 0.7085 (OUTLIER) cc_final: 0.6619 (m-10) REVERT: D 671 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.6832 (m-10) outliers start: 73 outliers final: 58 residues processed: 264 average time/residue: 0.0981 time to fit residues: 45.8493 Evaluate side-chains 266 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 200 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 501 MET Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain B residue 391 TRP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 501 MET Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain D residue 391 TRP Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 521 GLU Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 671 PHE Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 824 MET Chi-restraints excluded: chain B residue 1001 GLU Chi-restraints excluded: chain D residue 1001 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 219 optimal weight: 0.6980 chunk 192 optimal weight: 9.9990 chunk 262 optimal weight: 8.9990 chunk 234 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 279 optimal weight: 0.5980 chunk 252 optimal weight: 40.0000 chunk 246 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 705 HIS ** 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 = 0.4478 r_free = 0.4478 target = 0.200180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.173725 restraints weight = 30863.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.169342 restraints weight = 45231.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.168371 restraints weight = 48295.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.167573 restraints weight = 47938.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.166703 restraints weight = 41112.535| |-----------------------------------------------------------------------------| r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19534 Z= 0.100 Angle : 0.500 10.454 26938 Z= 0.258 Chirality : 0.043 0.303 3416 Planarity : 0.003 0.043 3546 Dihedral : 4.385 58.902 3260 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.18 % Favored : 94.75 % Rotamer: Outliers : 6.09 % Allowed : 27.62 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.16), residues: 3144 helix: 2.05 (0.15), residues: 1344 sheet: -1.27 (0.25), residues: 406 loop : -1.54 (0.16), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 763 TYR 0.027 0.001 TYR B 705 PHE 0.016 0.001 PHE A 654 TRP 0.016 0.001 TRP C 636 HIS 0.003 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00221 (19522) covalent geometry : angle 0.49915 (26914) SS BOND : bond 0.00099 ( 12) SS BOND : angle 1.02714 ( 24) hydrogen bonds : bond 0.03011 ( 1055) hydrogen bonds : angle 3.83057 ( 3075) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 206 time to evaluate : 0.775 Fit side-chains REVERT: B 391 TRP cc_start: 0.7155 (OUTLIER) cc_final: 0.6253 (t60) REVERT: B 554 PHE cc_start: 0.6990 (OUTLIER) cc_final: 0.6231 (m-10) REVERT: B 671 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.6858 (m-10) REVERT: C 478 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8448 (mp) REVERT: D 391 TRP cc_start: 0.7272 (OUTLIER) cc_final: 0.6014 (t60) REVERT: D 554 PHE cc_start: 0.7050 (OUTLIER) cc_final: 0.6603 (m-10) REVERT: D 671 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.6742 (m-10) REVERT: B 1001 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.7005 (tp30) outliers start: 65 outliers final: 48 residues processed: 263 average time/residue: 0.0994 time to fit residues: 46.4901 Evaluate side-chains 256 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 200 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain B residue 391 TRP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain D residue 391 TRP Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 671 PHE Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 824 MET Chi-restraints excluded: chain B residue 1001 GLU Chi-restraints excluded: chain D residue 1001 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 54 optimal weight: 4.9990 chunk 114 optimal weight: 0.0270 chunk 1 optimal weight: 50.0000 chunk 223 optimal weight: 3.9990 chunk 184 optimal weight: 50.0000 chunk 175 optimal weight: 30.0000 chunk 199 optimal weight: 0.8980 chunk 17 optimal weight: 40.0000 chunk 312 optimal weight: 0.8980 chunk 76 optimal weight: 0.0070 chunk 191 optimal weight: 40.0000 overall best weight: 1.1658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 705 HIS ** 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 = 0.4478 r_free = 0.4478 target = 0.199504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.171966 restraints weight = 30854.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.168698 restraints weight = 45985.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.166535 restraints weight = 46109.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.165888 restraints weight = 41701.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.164038 restraints weight = 37669.842| |-----------------------------------------------------------------------------| r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19534 Z= 0.127 Angle : 0.524 11.454 26938 Z= 0.272 Chirality : 0.043 0.317 3416 Planarity : 0.003 0.041 3546 Dihedral : 4.360 57.506 3257 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 5.81 % Allowed : 27.62 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.16), residues: 3144 helix: 2.05 (0.15), residues: 1346 sheet: -1.30 (0.26), residues: 398 loop : -1.47 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 763 TYR 0.025 0.001 TYR B 705 PHE 0.025 0.002 PHE C 533 TRP 0.015 0.001 TRP C 636 HIS 0.004 0.001 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00298 (19522) covalent geometry : angle 0.52401 (26914) SS BOND : bond 0.00230 ( 12) SS BOND : angle 0.70752 ( 24) hydrogen bonds : bond 0.03528 ( 1055) hydrogen bonds : angle 3.91581 ( 3075) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 202 time to evaluate : 0.722 Fit side-chains REVERT: A 478 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8528 (mp) REVERT: B 391 TRP cc_start: 0.7191 (OUTLIER) cc_final: 0.6271 (t60) REVERT: B 554 PHE cc_start: 0.6911 (OUTLIER) cc_final: 0.6236 (m-10) REVERT: B 671 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.6918 (m-10) REVERT: C 478 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8471 (mp) REVERT: D 391 TRP cc_start: 0.7318 (OUTLIER) cc_final: 0.6025 (t60) REVERT: D 554 PHE cc_start: 0.7089 (OUTLIER) cc_final: 0.6600 (m-10) REVERT: D 671 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.6782 (m-10) outliers start: 62 outliers final: 54 residues processed: 261 average time/residue: 0.0951 time to fit residues: 44.2194 Evaluate side-chains 262 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 200 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain B residue 391 TRP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain D residue 391 TRP Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 521 GLU Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 671 PHE Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 824 MET Chi-restraints excluded: chain B residue 1001 GLU Chi-restraints excluded: chain D residue 1001 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 7 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 234 optimal weight: 10.0000 chunk 275 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 220 optimal weight: 5.9990 chunk 113 optimal weight: 50.0000 chunk 121 optimal weight: 0.0970 chunk 258 optimal weight: 30.0000 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 HIS ** 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 = 0.4453 r_free = 0.4453 target = 0.196992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.170623 restraints weight = 30863.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.166015 restraints weight = 45630.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.164210 restraints weight = 50342.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.163436 restraints weight = 48933.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.162599 restraints weight = 40637.740| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 19534 Z= 0.202 Angle : 0.600 11.025 26938 Z= 0.316 Chirality : 0.045 0.324 3416 Planarity : 0.003 0.039 3546 Dihedral : 4.720 56.902 3257 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 6.27 % Allowed : 27.25 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.16), residues: 3144 helix: 1.92 (0.15), residues: 1346 sheet: -1.22 (0.27), residues: 370 loop : -1.52 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 763 TYR 0.035 0.002 TYR B 479 PHE 0.036 0.002 PHE C 533 TRP 0.016 0.002 TRP C 636 HIS 0.007 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00496 (19522) covalent geometry : angle 0.59983 (26914) SS BOND : bond 0.00303 ( 12) SS BOND : angle 0.92763 ( 24) hydrogen bonds : bond 0.04596 ( 1055) hydrogen bonds : angle 4.23758 ( 3075) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2939.18 seconds wall clock time: 51 minutes 2.82 seconds (3062.82 seconds total)