Starting phenix.real_space_refine on Sun Aug 24 11:06:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bib_44586/08_2025/9bib_44586.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bib_44586/08_2025/9bib_44586.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bib_44586/08_2025/9bib_44586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bib_44586/08_2025/9bib_44586.map" model { file = "/net/cci-nas-00/data/ceres_data/9bib_44586/08_2025/9bib_44586.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bib_44586/08_2025/9bib_44586.cif" } resolution = 3.81 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= 0.017 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 12236 2.51 5 N 3414 2.21 5 O 3539 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19269 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 4886 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 408} Link IDs: {'PTRANS': 34, 'TRANS': 760} Chain breaks: 2 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1451 Unresolved non-hydrogen angles: 1824 Unresolved non-hydrogen dihedrals: 1176 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': 26, 'PHE:plan': 8, 'ASP:plan': 29, 'TYR:plan': 11, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 841 Chain: "B" Number of atoms: 4733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 4733 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 431} Link IDs: {'PTRANS': 29, 'TRANS': 759} Chain breaks: 2 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1571 Unresolved non-hydrogen angles: 2003 Unresolved non-hydrogen dihedrals: 1313 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'ASP:plan': 45, 'GLU:plan': 45, 'HIS:plan': 9, 'PHE:plan': 18, 'ARG:plan': 19, 'ASN:plan1': 24, 'GLN:plan1': 21, 'TYR:plan': 19, 'TRP:plan': 7} Unresolved non-hydrogen planarities: 915 Chain: "C" Number of atoms: 4885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 4885 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 408} Link IDs: {'PTRANS': 34, 'TRANS': 760} Chain breaks: 2 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1452 Unresolved non-hydrogen angles: 1824 Unresolved non-hydrogen dihedrals: 1178 Unresolved non-hydrogen chiralities: 110 Planarities with less than four sites: {'ASN:plan1': 29, 'ARG:plan': 36, 'HIS:plan': 13, 'GLU:plan': 46, 'GLN:plan1': 26, 'PHE:plan': 8, 'ASP:plan': 29, 'TYR:plan': 11, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 841 Chain: "D" Number of atoms: 4735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 4735 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 431} Link IDs: {'PTRANS': 29, 'TRANS': 759} Chain breaks: 2 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1568 Unresolved non-hydrogen angles: 1999 Unresolved non-hydrogen dihedrals: 1309 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'ASP:plan': 45, 'GLU:plan': 45, 'HIS:plan': 9, 'PHE:plan': 17, 'ARG:plan': 19, 'ASN:plan1': 24, 'GLN:plan1': 22, 'TYR:plan': 19, 'TRP:plan': 7} Unresolved non-hydrogen planarities: 913 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} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 4.28, per 1000 atoms: 0.22 Number of scatterers: 19269 At special positions: 0 Unit cell: (125.706, 149.814, 185.115, 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 3539 8.00 N 3414 7.00 C 12236 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=2.03 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=2.03 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: 1.43 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 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 44.4% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 103 through 112 removed outlier: 3.696A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 158 removed outlier: 4.248A pdb=" N SER A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 187 removed outlier: 3.702A 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: 3.806A pdb=" N ALA A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 4.012A 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 260 removed outlier: 3.972A pdb=" N LEU A 259 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG A 260 " --> pdb=" O ASN A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 256 through 260' Processing helix chain 'A' and resid 277 through 296 removed outlier: 3.590A pdb=" N ILE A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 327 removed outlier: 4.589A pdb=" N LEU A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 321 " --> pdb=" O THR A 317 " (cutoff:3.500A) 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 525 Processing helix chain 'A' and resid 559 through 583 removed outlier: 3.668A pdb=" N VAL A 570 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N HIS A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 616 removed outlier: 3.529A pdb=" N LEU A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 654 removed outlier: 3.734A pdb=" N PHE A 654 " --> pdb=" O ASN A 650 " (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 695 through 698 removed outlier: 6.069A pdb=" N GLU A 698 " --> pdb=" O ARG A 695 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 695 through 698' Processing helix chain 'A' and resid 699 through 708 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: 4.012A pdb=" N GLN A 770 " --> pdb=" O SER A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'A' and resid 811 through 841 removed outlier: 4.205A pdb=" N GLY A 815 " --> pdb=" O GLU A 811 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 56 Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.549A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 120 removed outlier: 4.302A pdb=" N ALA B 109 " --> pdb=" O GLN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'B' and resid 149 through 164 Processing helix chain 'B' and resid 176 through 192 Processing helix chain 'B' and resid 212 through 221 removed outlier: 3.589A 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 259 through 264 removed outlier: 4.284A pdb=" N ALA B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 259 through 264' Processing helix chain 'B' and resid 288 through 311 Processing helix chain 'B' and resid 325 through 330 removed outlier: 3.922A pdb=" N ARG B 328 " --> pdb=" O HIS B 325 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE B 329 " --> pdb=" O GLU B 326 " (cutoff:3.500A) removed outlier: 4.086A 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: 3.528A pdb=" N ASN B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 473 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 removed outlier: 3.655A pdb=" N LEU B 551 " --> pdb=" O SER B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 581 Processing helix chain 'B' and resid 601 through 614 removed outlier: 3.574A pdb=" N LEU B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 647 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 Processing helix chain 'B' and resid 699 through 707 Processing helix chain 'B' and resid 708 through 710 No H-bonds generated for 'chain 'B' and resid 708 through 710' Processing helix chain 'B' and resid 713 through 724 Processing helix chain 'B' and resid 733 through 742 Processing helix chain 'B' and resid 771 through 787 removed outlier: 4.385A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.704A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 844 removed outlier: 3.815A pdb=" N TYR B 823 " --> pdb=" O ALA B 819 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET B 824 " --> pdb=" O GLY B 820 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TRP B 844 " --> pdb=" O HIS B 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 50 Processing helix chain 'C' and resid 70 through 86 Processing helix chain 'C' and resid 103 through 112 removed outlier: 3.740A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 158 removed outlier: 4.259A pdb=" N SER C 148 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 187 removed outlier: 3.716A 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: 3.793A pdb=" N ALA C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 4.041A 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 260 removed outlier: 3.971A pdb=" N LEU C 259 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG C 260 " --> pdb=" O ASN C 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 256 through 260' Processing helix chain 'C' and resid 277 through 296 removed outlier: 3.558A pdb=" N ILE C 281 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 327 removed outlier: 4.472A pdb=" N LEU C 320 " --> pdb=" O LYS C 316 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE C 321 " --> pdb=" O THR C 317 " (cutoff:3.500A) 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 525 Processing helix chain 'C' and resid 559 through 583 removed outlier: 3.799A pdb=" N TRP C 563 " --> pdb=" O GLN C 559 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU C 564 " --> pdb=" O SER C 560 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C 565 " --> pdb=" O THR C 561 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 616 removed outlier: 3.763A pdb=" N LEU C 614 " --> pdb=" O SER C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 655 Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 694 Processing helix chain 'C' and resid 695 through 698 removed outlier: 6.128A pdb=" N GLU C 698 " --> pdb=" O ARG C 695 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 695 through 698' Processing helix chain 'C' and resid 699 through 708 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: 3.630A pdb=" N GLN C 770 " --> pdb=" O SER C 766 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER C 773 " --> pdb=" O LYS C 769 " (cutoff:3.500A) removed outlier: 3.539A 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 811 through 840 removed outlier: 4.029A pdb=" N GLY C 815 " --> pdb=" O GLU C 811 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS C 840 " --> pdb=" O ALA C 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 56 Processing helix chain 'D' and resid 77 through 92 removed outlier: 4.223A pdb=" N ARG D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 120 removed outlier: 4.305A 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: 3.698A pdb=" N ASN D 192 " --> pdb=" O SER D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 221 removed outlier: 3.581A 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: 3.810A pdb=" N ARG D 328 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE D 329 " --> pdb=" O GLU D 326 " (cutoff:3.500A) removed outlier: 4.084A 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: 3.521A pdb=" N ASN D 336 " --> pdb=" O SER D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 473 removed outlier: 3.527A pdb=" N SER D 471 " --> pdb=" O LYS D 467 " (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: 3.770A pdb=" N ASN D 615 " --> pdb=" O GLY D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 647 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 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 771 through 787 removed outlier: 4.381A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 797 removed outlier: 3.578A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 819 removed outlier: 3.525A pdb=" N MET D 818 " --> pdb=" O ASP D 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 844 removed outlier: 3.612A pdb=" N TRP D 844 " --> pdb=" O HIS D 840 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 removed outlier: 7.109A pdb=" N ALA A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 removed outlier: 7.207A pdb=" N ILE A 163 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N LEU A 195 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N SER A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU A 166 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 271 removed outlier: 3.794A pdb=" N GLY A 268 " --> pdb=" O MET A 354 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET A 354 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 366 " --> pdb=" O ILE A 373 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 478 removed outlier: 7.225A pdb=" N LEU A 398 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N HIS A 477 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 6.051A 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: 3.667A pdb=" N TYR A 456 " --> pdb=" O TYR A 410 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 412 " --> pdb=" O CYS A 454 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 487 through 488 Processing sheet with id=AA7, first strand: chain 'A' and resid 681 through 682 removed outlier: 3.606A pdb=" N ALA A 682 " --> pdb=" O ALA A 728 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE A 730 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 542 " --> pdb=" O VAL A 747 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 70 through 73 removed outlier: 8.447A pdb=" N VAL B 71 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL B 39 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N MET B 73 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LEU B 41 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLY B 36 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE B 123 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL B 97 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY B 125 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N PHE B 99 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N HIS B 127 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP B 101 " --> pdb=" O HIS B 127 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE B 123 " --> pdb=" O PHE B 144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 198 through 203 removed outlier: 8.216A pdb=" N PHE B 169 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 9.492A pdb=" N LEU B 203 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR B 231 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N VAL B 258 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 9.911A pdb=" N TYR B 282 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 279 " --> pdb=" O ILE B 365 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 362 " --> pdb=" O TRP B 379 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY B 377 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU B 366 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 5.978A 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: 3.602A pdb=" N THR B 410 " --> pdb=" O TYR B 479 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N SER B 407 " --> pdb=" O MET B 508 " (cutoff:3.500A) removed outlier: 3.529A 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: 3.974A pdb=" N ILE B 453 " --> pdb=" O LYS B 438 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL B 434 " --> pdb=" O CYS B 457 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 488 through 490 removed outlier: 4.149A pdb=" N LYS B 488 " --> pdb=" O ASN B 495 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN B 495 " --> pdb=" O LYS B 488 " (cutoff:3.500A) removed outlier: 3.824A 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: 4.046A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 535 " --> pdb=" O TYR B 731 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL B 538 " --> pdb=" O VAL B 749 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL B 749 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 729 through 732 removed outlier: 4.046A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 535 " --> pdb=" O TYR B 731 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ILE B 534 " --> pdb=" O ALA B 758 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ALA B 758 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 64 through 65 removed outlier: 7.044A pdb=" N ALA C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 193 through 197 removed outlier: 7.187A pdb=" N ILE C 163 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N LEU C 195 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE C 164 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU C 166 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 267 through 268 removed outlier: 3.785A pdb=" N GLY C 268 " --> pdb=" O MET C 354 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET C 354 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 6.876A 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: 7.071A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 5.992A 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 413 removed outlier: 3.675A pdb=" N TYR C 456 " --> pdb=" O TYR C 410 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS C 412 " --> pdb=" O CYS C 454 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 487 through 488 removed outlier: 3.578A pdb=" N GLU C 488 " --> pdb=" O GLU C 497 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 681 through 682 removed outlier: 3.587A pdb=" N ALA C 682 " --> pdb=" O ALA C 728 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE C 730 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE C 729 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP C 731 " --> pdb=" O THR C 539 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 70 through 73 removed outlier: 8.399A pdb=" N VAL D 71 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL D 39 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N MET D 73 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LEU D 41 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLY D 36 " --> pdb=" O ILE D 94 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE D 123 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL D 97 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLY D 125 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N PHE D 99 " --> pdb=" O GLY D 125 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N HIS D 127 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP D 101 " --> pdb=" O HIS D 127 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE D 123 " --> pdb=" O PHE D 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 198 through 203 removed outlier: 8.251A pdb=" N PHE D 169 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 9.551A pdb=" N LEU D 203 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR D 231 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL D 258 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 9.960A pdb=" N TYR D 282 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER D 279 " --> pdb=" O ILE D 365 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 362 " --> pdb=" O TRP D 379 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY D 377 " --> pdb=" O ILE D 364 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU D 366 " --> pdb=" O ARG D 375 " (cutoff:3.500A) removed outlier: 6.017A 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: 6.928A pdb=" N LEU D 406 " --> pdb=" O ASP D 477 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N TYR D 479 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE D 408 " --> pdb=" O TYR D 479 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL D 409 " --> pdb=" O MET D 508 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 418 through 420 removed outlier: 3.971A pdb=" N ILE D 453 " --> pdb=" O LYS D 438 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL D 434 " --> pdb=" O CYS D 457 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 488 through 490 removed outlier: 4.085A pdb=" N LYS D 488 " --> pdb=" O ASN D 495 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASN D 495 " --> pdb=" O LYS D 488 " (cutoff:3.500A) removed outlier: 3.842A 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: 3.932A pdb=" N TYR D 731 " --> pdb=" O SER D 535 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER D 535 " --> pdb=" O TYR D 731 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL D 538 " --> pdb=" O VAL D 749 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL D 749 " --> pdb=" O VAL D 538 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 729 through 732 removed outlier: 3.932A pdb=" N TYR D 731 " --> pdb=" O SER D 535 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER D 535 " --> pdb=" O TYR D 731 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ILE D 534 " --> pdb=" O ALA D 758 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ALA D 758 " --> pdb=" O ILE D 534 " (cutoff:3.500A) 1046 hydrogen bonds defined for protein. 3057 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: 2.72 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 3293 1.25 - 1.39: 4580 1.39 - 1.53: 10888 1.53 - 1.68: 683 1.68 - 1.82: 132 Bond restraints: 19576 Sorted by residual: bond pdb=" C PRO B 623 " pdb=" N LYS B 624 " ideal model delta sigma weight residual 1.331 1.587 -0.256 1.51e-02 4.39e+03 2.87e+02 bond pdb=" CA SER B 617 " pdb=" CB SER B 617 " ideal model delta sigma weight residual 1.539 1.371 0.168 1.20e-02 6.94e+03 1.96e+02 bond pdb=" C VAL D 618 " pdb=" O VAL D 618 " ideal model delta sigma weight residual 1.240 1.108 0.131 1.26e-02 6.30e+03 1.09e+02 bond pdb=" C PHE D 614 " pdb=" O PHE D 614 " ideal model delta sigma weight residual 1.237 1.114 0.123 1.19e-02 7.06e+03 1.06e+02 bond pdb=" CA SER D 617 " pdb=" CB SER D 617 " ideal model delta sigma weight residual 1.538 1.423 0.115 1.35e-02 5.49e+03 7.31e+01 ... (remaining 19571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.96: 26878 3.96 - 7.91: 81 7.91 - 11.87: 17 11.87 - 15.82: 7 15.82 - 19.78: 1 Bond angle restraints: 26984 Sorted by residual: angle pdb=" CA PHE D 614 " pdb=" C PHE D 614 " pdb=" O PHE D 614 " ideal model delta sigma weight residual 120.42 107.93 12.49 1.06e+00 8.90e-01 1.39e+02 angle pdb=" CA PHE D 614 " pdb=" CB PHE D 614 " pdb=" CG PHE D 614 " ideal model delta sigma weight residual 113.80 102.76 11.04 1.00e+00 1.00e+00 1.22e+02 angle pdb=" C LEU B 612 " pdb=" N VAL B 613 " pdb=" CA VAL B 613 " ideal model delta sigma weight residual 121.77 107.02 14.75 1.44e+00 4.82e-01 1.05e+02 angle pdb=" C ASN D 615 " pdb=" CA ASN D 615 " pdb=" CB ASN D 615 " ideal model delta sigma weight residual 110.42 90.64 19.78 1.99e+00 2.53e-01 9.88e+01 angle pdb=" C LEU D 612 " pdb=" N VAL D 613 " pdb=" CA VAL D 613 " ideal model delta sigma weight residual 121.35 105.90 15.45 1.58e+00 4.01e-01 9.56e+01 ... (remaining 26979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.99: 10839 11.99 - 23.99: 285 23.99 - 35.98: 92 35.98 - 47.98: 37 47.98 - 59.97: 12 Dihedral angle restraints: 11265 sinusoidal: 2137 harmonic: 9128 Sorted by residual: dihedral pdb=" C ASN D 615 " pdb=" N ASN D 615 " pdb=" CA ASN D 615 " pdb=" CB ASN D 615 " ideal model delta harmonic sigma weight residual -122.60 -95.95 -26.65 0 2.50e+00 1.60e-01 1.14e+02 dihedral pdb=" C PHE C 654 " pdb=" N PHE C 654 " pdb=" CA PHE C 654 " pdb=" CB PHE C 654 " ideal model delta harmonic sigma weight residual -122.60 -149.01 26.41 0 2.50e+00 1.60e-01 1.12e+02 dihedral pdb=" N PHE C 654 " pdb=" C PHE C 654 " pdb=" CA PHE C 654 " pdb=" CB PHE C 654 " ideal model delta harmonic sigma weight residual 122.80 146.14 -23.34 0 2.50e+00 1.60e-01 8.72e+01 ... (remaining 11262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.207: 3398 0.207 - 0.414: 13 0.414 - 0.621: 2 0.621 - 0.828: 1 0.828 - 1.036: 3 Chirality restraints: 3417 Sorted by residual: chirality pdb=" CA PHE C 654 " pdb=" N PHE C 654 " pdb=" C PHE C 654 " pdb=" CB PHE C 654 " both_signs ideal model delta sigma weight residual False 2.51 1.47 1.04 2.00e-01 2.50e+01 2.68e+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 1.52 0.99 2.00e-01 2.50e+01 2.47e+01 chirality pdb=" CA PHE D 614 " pdb=" N PHE D 614 " pdb=" C PHE D 614 " pdb=" CB PHE D 614 " both_signs ideal model delta sigma weight residual False 2.51 1.61 0.90 2.00e-01 2.50e+01 2.05e+01 ... (remaining 3414 not shown) Planarity restraints: 3552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 614 " 0.023 2.00e-02 2.50e+03 5.19e-02 2.70e+01 pdb=" C PHE D 614 " -0.090 2.00e-02 2.50e+03 pdb=" O PHE D 614 " 0.034 2.00e-02 2.50e+03 pdb=" N ASN D 615 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 619 " 0.025 2.00e-02 2.50e+03 5.18e-02 2.69e+01 pdb=" C PRO D 619 " -0.090 2.00e-02 2.50e+03 pdb=" O PRO D 619 " 0.034 2.00e-02 2.50e+03 pdb=" N VAL D 620 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 643 " -0.021 2.00e-02 2.50e+03 4.44e-02 1.98e+01 pdb=" C LEU D 643 " 0.077 2.00e-02 2.50e+03 pdb=" O LEU D 643 " -0.028 2.00e-02 2.50e+03 pdb=" N ALA D 644 " -0.027 2.00e-02 2.50e+03 ... (remaining 3549 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1519 2.74 - 3.28: 18228 3.28 - 3.82: 29862 3.82 - 4.36: 27331 4.36 - 4.90: 52467 Nonbonded interactions: 129407 Sorted by model distance: nonbonded pdb=" O THR B 647 " pdb=" OG1 THR B 647 " model vdw 2.200 3.040 nonbonded pdb=" O LEU D 612 " pdb=" CA VAL D 613 " model vdw 2.263 2.776 nonbonded pdb=" O LEU B 612 " pdb=" CA VAL B 613 " model vdw 2.282 2.776 nonbonded pdb=" OE1 GLU D 413 " pdb=" OG SER D 512 " model vdw 2.303 3.040 nonbonded pdb=" CB ASN D 615 " pdb=" N ASN D 616 " model vdw 2.309 2.816 ... (remaining 129402 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 789 or (resid 790 and (name N or name CA or nam \ e C or name O or name CB )) or resid 791 through 831 or (resid 832 and (name N o \ r name CA or name C or name O or name CB )) or resid 833 through 1001)) selection = (chain 'C' and (resid 25 through 816 or (resid 817 through 819 and (name N or na \ me CA or name C or name O or name CB )) or resid 820 through 1001)) } ncs_group { reference = (chain 'B' and (resid 34 through 576 or (resid 577 through 581 and (name N or na \ me CA or name C or name O or name CB )) or resid 582 through 655 or (resid 656 t \ hrough 658 and (name N or name CA or name C or name O or name CB )) or resid 659 \ through 1001)) selection = (chain 'D' and (resid 34 through 562 or (resid 563 and (name N or name CA or nam \ e C or name O or name CB )) or resid 564 through 835 or (resid 836 and (name N o \ r name CA or name C or name O or name CB )) or resid 837 through 1001)) } 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: 4.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.700 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 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 : 0.004 0.256 19588 Z= 0.316 Angle : 0.625 19.781 27008 Z= 0.413 Chirality : 0.055 1.036 3417 Planarity : 0.004 0.095 3552 Dihedral : 7.502 59.972 5309 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.99 % Favored : 96.91 % Rotamer: Outliers : 4.65 % Allowed : 7.43 % Favored : 87.92 % Cbeta Deviations : 0.41 % 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: -2.18 (0.13), residues: 3144 helix: -0.02 (0.13), residues: 1352 sheet: -1.28 (0.28), residues: 312 loop : -2.96 (0.13), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 519 TYR 0.004 0.000 TYR D 731 PHE 0.072 0.001 PHE D 614 TRP 0.006 0.000 TRP C 636 HIS 0.001 0.000 HIS D 703 Details of bonding type rmsd covalent geometry : bond 0.00445 (19576) covalent geometry : angle 0.62500 (26984) SS BOND : bond 0.00082 ( 12) SS BOND : angle 0.44953 ( 24) hydrogen bonds : bond 0.15982 ( 1042) hydrogen bonds : angle 6.02678 ( 3057) *********************** 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 452 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 402 time to evaluate : 0.617 Fit side-chains REVERT: A 807 THR cc_start: 0.8184 (t) cc_final: 0.7926 (m) REVERT: B 607 TRP cc_start: 0.7682 (t-100) cc_final: 0.5152 (t60) REVERT: B 823 TYR cc_start: 0.6946 (m-80) cc_final: 0.6718 (m-10) REVERT: C 166 LEU cc_start: 0.8403 (tt) cc_final: 0.8194 (mp) REVERT: C 584 SER cc_start: 0.5077 (t) cc_final: 0.4751 (p) REVERT: D 628 SER cc_start: 0.7181 (p) cc_final: 0.6880 (t) outliers start: 50 outliers final: 17 residues processed: 434 average time/residue: 0.1117 time to fit residues: 77.3121 Evaluate side-chains 261 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 244 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 617 SER Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 821 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 0.0570 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.0020 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 40.0000 chunk 298 optimal weight: 7.9990 overall best weight: 1.8110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 771 GLN B 486 HIS B 615 ASN B 703 HIS C 405 GLN C 477 HIS C 509 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.175822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.142812 restraints weight = 36370.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.139114 restraints weight = 55808.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.135990 restraints weight = 49818.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.134835 restraints weight = 51270.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.134062 restraints weight = 42413.705| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19588 Z= 0.173 Angle : 0.558 9.405 27008 Z= 0.305 Chirality : 0.045 0.184 3417 Planarity : 0.004 0.056 3552 Dihedral : 4.241 58.432 3263 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.61 % Favored : 95.32 % Rotamer: Outliers : 6.88 % Allowed : 15.33 % Favored : 77.79 % 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: -0.91 (0.15), residues: 3144 helix: 1.23 (0.14), residues: 1360 sheet: -0.85 (0.28), residues: 338 loop : -2.47 (0.14), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 505 TYR 0.027 0.002 TYR C 410 PHE 0.048 0.003 PHE A 533 TRP 0.018 0.002 TRP A 498 HIS 0.010 0.002 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00403 (19576) covalent geometry : angle 0.55583 (26984) SS BOND : bond 0.00867 ( 12) SS BOND : angle 1.75623 ( 24) hydrogen bonds : bond 0.04570 ( 1042) hydrogen bonds : angle 4.26557 ( 3057) *********************** 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 330 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 256 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 348 PHE cc_start: 0.8065 (m-10) cc_final: 0.7830 (m-80) REVERT: A 544 LYS cc_start: 0.6468 (OUTLIER) cc_final: 0.5984 (mtpp) REVERT: A 607 MET cc_start: 0.8360 (tpp) cc_final: 0.8126 (tpp) REVERT: B 567 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8404 (mt) REVERT: C 166 LEU cc_start: 0.8882 (tt) cc_final: 0.8449 (mp) REVERT: C 774 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8492 (mp) REVERT: D 476 TYR cc_start: 0.7869 (p90) cc_final: 0.7567 (p90) outliers start: 74 outliers final: 38 residues processed: 310 average time/residue: 0.0882 time to fit residues: 47.2431 Evaluate side-chains 259 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 687 SER Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 774 LEU Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 521 GLU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 751 ILE Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 837 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 106 optimal weight: 50.0000 chunk 281 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 41 optimal weight: 0.3980 chunk 235 optimal weight: 1.9990 chunk 243 optimal weight: 50.0000 chunk 268 optimal weight: 50.0000 chunk 54 optimal weight: 1.9990 chunk 295 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 288 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 705 HIS D 662 GLN D 703 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.175575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.148474 restraints weight = 36552.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.148011 restraints weight = 63225.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.146181 restraints weight = 53278.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.143593 restraints weight = 54069.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.143376 restraints weight = 54892.702| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19588 Z= 0.123 Angle : 0.476 8.294 27008 Z= 0.259 Chirality : 0.042 0.155 3417 Planarity : 0.003 0.054 3552 Dihedral : 3.692 53.916 3248 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.36 % Favored : 95.58 % Rotamer: Outliers : 5.76 % Allowed : 17.29 % Favored : 76.95 % 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: -0.34 (0.15), residues: 3144 helix: 1.78 (0.15), residues: 1370 sheet: -0.80 (0.28), residues: 348 loop : -2.21 (0.14), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 694 TYR 0.020 0.001 TYR A 681 PHE 0.024 0.002 PHE D 114 TRP 0.015 0.001 TRP B 607 HIS 0.005 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00283 (19576) covalent geometry : angle 0.47465 (26984) SS BOND : bond 0.00317 ( 12) SS BOND : angle 1.28579 ( 24) hydrogen bonds : bond 0.03627 ( 1042) hydrogen bonds : angle 3.92099 ( 3057) *********************** 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 303 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 241 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 544 LYS cc_start: 0.6524 (OUTLIER) cc_final: 0.6135 (mtpp) REVERT: A 607 MET cc_start: 0.8240 (tpp) cc_final: 0.7895 (tpp) REVERT: A 726 LEU cc_start: 0.5870 (OUTLIER) cc_final: 0.5670 (mt) REVERT: B 705 TYR cc_start: 0.7600 (t80) cc_final: 0.7156 (t80) REVERT: C 166 LEU cc_start: 0.8853 (tt) cc_final: 0.8456 (mp) REVERT: D 437 GLN cc_start: 0.7774 (mt0) cc_final: 0.7429 (mp10) REVERT: D 476 TYR cc_start: 0.7730 (p90) cc_final: 0.7473 (p90) REVERT: D 554 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7492 (m-10) outliers start: 62 outliers final: 42 residues processed: 287 average time/residue: 0.0833 time to fit residues: 41.3392 Evaluate side-chains 266 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 221 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain B residue 832 SER Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 768 LYS Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 837 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 6 optimal weight: 0.7980 chunk 129 optimal weight: 0.2980 chunk 214 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 168 optimal weight: 20.0000 chunk 215 optimal weight: 2.9990 chunk 278 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 chunk 30 optimal weight: 0.0370 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 662 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.177396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.145996 restraints weight = 36525.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.142848 restraints weight = 56479.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.140796 restraints weight = 47185.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.140292 restraints weight = 45465.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.139409 restraints weight = 38910.402| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19588 Z= 0.087 Angle : 0.448 9.645 27008 Z= 0.239 Chirality : 0.041 0.169 3417 Planarity : 0.003 0.044 3552 Dihedral : 3.475 51.848 3248 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.45 % Favored : 95.48 % Rotamer: Outliers : 5.30 % Allowed : 18.03 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.07 (0.16), residues: 3144 helix: 2.13 (0.15), residues: 1360 sheet: -0.65 (0.29), residues: 354 loop : -1.96 (0.15), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 694 TYR 0.015 0.001 TYR A 681 PHE 0.024 0.001 PHE D 114 TRP 0.013 0.001 TRP B 607 HIS 0.003 0.001 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00188 (19576) covalent geometry : angle 0.44324 (26984) SS BOND : bond 0.00352 ( 12) SS BOND : angle 2.16241 ( 24) hydrogen bonds : bond 0.02841 ( 1042) hydrogen bonds : angle 3.66708 ( 3057) *********************** 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 301 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 244 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 568 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7829 (tm) REVERT: A 607 MET cc_start: 0.8250 (tpp) cc_final: 0.7928 (tpp) REVERT: B 456 CYS cc_start: 0.6459 (m) cc_final: 0.6186 (m) REVERT: B 567 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8272 (mt) REVERT: B 705 TYR cc_start: 0.7595 (t80) cc_final: 0.7080 (t80) REVERT: C 166 LEU cc_start: 0.8916 (tt) cc_final: 0.8449 (mp) REVERT: D 476 TYR cc_start: 0.7621 (p90) cc_final: 0.7325 (p90) REVERT: D 554 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7460 (m-10) outliers start: 57 outliers final: 38 residues processed: 285 average time/residue: 0.0885 time to fit residues: 43.0872 Evaluate side-chains 262 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 221 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 768 LYS Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 837 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 221 optimal weight: 3.9990 chunk 262 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 108 optimal weight: 40.0000 chunk 192 optimal weight: 0.0870 chunk 203 optimal weight: 8.9990 chunk 103 optimal weight: 0.0060 chunk 128 optimal weight: 4.9990 chunk 224 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 3 optimal weight: 40.0000 overall best weight: 2.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 662 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.170912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.140945 restraints weight = 36174.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.138980 restraints weight = 55136.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.136117 restraints weight = 50560.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.134639 restraints weight = 54066.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.133162 restraints weight = 48789.573| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 19588 Z= 0.211 Angle : 0.579 10.961 27008 Z= 0.315 Chirality : 0.045 0.177 3417 Planarity : 0.004 0.063 3552 Dihedral : 4.177 48.543 3248 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.47 % Favored : 94.47 % Rotamer: Outliers : 7.06 % Allowed : 18.40 % Favored : 74.54 % 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: -0.05 (0.15), residues: 3144 helix: 1.96 (0.15), residues: 1365 sheet: -0.66 (0.29), residues: 335 loop : -1.96 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 694 TYR 0.021 0.002 TYR C 410 PHE 0.041 0.003 PHE C 533 TRP 0.015 0.002 TRP B 607 HIS 0.006 0.001 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00507 (19576) covalent geometry : angle 0.57637 (26984) SS BOND : bond 0.00277 ( 12) SS BOND : angle 2.01542 ( 24) hydrogen bonds : bond 0.04955 ( 1042) hydrogen bonds : angle 4.13557 ( 3057) *********************** 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 294 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 218 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 568 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7878 (tm) REVERT: A 607 MET cc_start: 0.8321 (tpp) cc_final: 0.7934 (tpp) REVERT: A 693 PHE cc_start: 0.7355 (OUTLIER) cc_final: 0.7043 (t80) REVERT: A 709 HIS cc_start: 0.6786 (OUTLIER) cc_final: 0.5464 (p90) REVERT: B 554 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.8334 (m-10) REVERT: B 567 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8322 (mt) REVERT: B 654 MET cc_start: 0.8492 (mtt) cc_final: 0.8198 (mtt) REVERT: B 705 TYR cc_start: 0.7986 (t80) cc_final: 0.7463 (t80) REVERT: C 166 LEU cc_start: 0.8879 (tt) cc_final: 0.8380 (mp) REVERT: D 437 GLN cc_start: 0.7913 (mt0) cc_final: 0.7609 (mp10) REVERT: D 554 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7599 (m-10) outliers start: 76 outliers final: 53 residues processed: 276 average time/residue: 0.0842 time to fit residues: 40.7106 Evaluate side-chains 265 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 206 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 751 ILE Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 837 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 37 optimal weight: 1.9990 chunk 191 optimal weight: 9.9990 chunk 228 optimal weight: 0.9980 chunk 23 optimal weight: 20.0000 chunk 67 optimal weight: 6.9990 chunk 130 optimal weight: 0.3980 chunk 99 optimal weight: 50.0000 chunk 36 optimal weight: 20.0000 chunk 47 optimal weight: 0.9980 chunk 195 optimal weight: 0.8980 chunk 18 optimal weight: 30.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 616 ASN ** D 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 662 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.173639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.146107 restraints weight = 36076.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.143463 restraints weight = 66498.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.142313 restraints weight = 64313.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.141632 restraints weight = 54237.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.140821 restraints weight = 51854.233| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19588 Z= 0.112 Angle : 0.485 10.841 27008 Z= 0.259 Chirality : 0.042 0.156 3417 Planarity : 0.003 0.064 3552 Dihedral : 3.822 47.364 3248 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.80 % Favored : 95.13 % Rotamer: Outliers : 6.04 % Allowed : 19.33 % Favored : 74.63 % 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: 0.21 (0.16), residues: 3144 helix: 2.15 (0.15), residues: 1361 sheet: -0.61 (0.28), residues: 355 loop : -1.76 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 694 TYR 0.013 0.001 TYR A 681 PHE 0.023 0.002 PHE D 114 TRP 0.020 0.001 TRP B 607 HIS 0.003 0.001 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00257 (19576) covalent geometry : angle 0.48264 (26984) SS BOND : bond 0.00336 ( 12) SS BOND : angle 1.71220 ( 24) hydrogen bonds : bond 0.03509 ( 1042) hydrogen bonds : angle 3.74524 ( 3057) *********************** 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 290 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 225 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 555 MET cc_start: 0.7992 (tpp) cc_final: 0.7621 (tpp) REVERT: A 568 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7706 (tm) REVERT: A 607 MET cc_start: 0.8246 (tpp) cc_final: 0.7825 (tpp) REVERT: A 693 PHE cc_start: 0.7321 (OUTLIER) cc_final: 0.6981 (t80) REVERT: B 567 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8198 (mt) REVERT: B 705 TYR cc_start: 0.7867 (t80) cc_final: 0.7419 (t80) REVERT: C 166 LEU cc_start: 0.8839 (tt) cc_final: 0.8382 (mp) REVERT: C 269 LEU cc_start: 0.7253 (tp) cc_final: 0.7036 (tp) REVERT: D 134 MET cc_start: 0.6628 (tpt) cc_final: 0.5692 (tpt) REVERT: D 554 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7589 (m-10) REVERT: D 666 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8424 (pp) outliers start: 65 outliers final: 48 residues processed: 275 average time/residue: 0.0798 time to fit residues: 38.6585 Evaluate side-chains 261 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 208 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain B residue 832 SER Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 837 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 75 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 230 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 106 optimal weight: 50.0000 chunk 191 optimal weight: 8.9990 chunk 0 optimal weight: 80.0000 chunk 52 optimal weight: 0.1980 chunk 245 optimal weight: 50.0000 chunk 260 optimal weight: 0.0770 chunk 5 optimal weight: 8.9990 overall best weight: 2.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 HIS C 404 HIS D 662 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.174119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.154979 restraints weight = 37198.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.153408 restraints weight = 56632.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.150811 restraints weight = 59066.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.150092 restraints weight = 67128.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.148937 restraints weight = 55707.860| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 19588 Z= 0.194 Angle : 0.572 10.492 27008 Z= 0.307 Chirality : 0.044 0.174 3417 Planarity : 0.004 0.074 3552 Dihedral : 4.180 45.556 3247 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.85 % Favored : 94.08 % Rotamer: Outliers : 6.78 % Allowed : 19.61 % Favored : 73.61 % 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: 0.13 (0.16), residues: 3144 helix: 2.03 (0.15), residues: 1361 sheet: -0.63 (0.29), residues: 354 loop : -1.75 (0.16), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 694 TYR 0.020 0.001 TYR B 479 PHE 0.037 0.002 PHE C 533 TRP 0.019 0.001 TRP B 607 HIS 0.007 0.001 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00467 (19576) covalent geometry : angle 0.56978 (26984) SS BOND : bond 0.00699 ( 12) SS BOND : angle 1.95250 ( 24) hydrogen bonds : bond 0.04693 ( 1042) hydrogen bonds : angle 4.06107 ( 3057) *********************** 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 282 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 209 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 568 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7687 (tm) REVERT: A 709 HIS cc_start: 0.6978 (OUTLIER) cc_final: 0.5918 (p90) REVERT: B 567 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7951 (mt) REVERT: B 748 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7626 (mt) REVERT: C 166 LEU cc_start: 0.8675 (tt) cc_final: 0.8291 (mp) REVERT: D 134 MET cc_start: 0.6433 (tpt) cc_final: 0.5530 (tpt) REVERT: D 554 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7507 (m-10) REVERT: D 631 MET cc_start: 0.6324 (tpt) cc_final: 0.6101 (tpt) outliers start: 73 outliers final: 57 residues processed: 264 average time/residue: 0.0874 time to fit residues: 40.7502 Evaluate side-chains 266 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 204 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 832 SER Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 751 ILE Chi-restraints excluded: chain D residue 768 LYS Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 837 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 178 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 250 optimal weight: 40.0000 chunk 147 optimal weight: 0.7980 chunk 99 optimal weight: 50.0000 chunk 120 optimal weight: 5.9990 chunk 191 optimal weight: 50.0000 chunk 73 optimal weight: 0.9980 chunk 223 optimal weight: 1.9990 chunk 189 optimal weight: 8.9990 chunk 222 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 662 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.174531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.155224 restraints weight = 37131.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.153682 restraints weight = 57211.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.151798 restraints weight = 51963.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.150676 restraints weight = 60770.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.149970 restraints weight = 58881.186| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19588 Z= 0.168 Angle : 0.545 9.611 27008 Z= 0.293 Chirality : 0.044 0.171 3417 Planarity : 0.004 0.066 3552 Dihedral : 4.144 44.008 3247 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.57 % Favored : 94.37 % Rotamer: Outliers : 6.41 % Allowed : 20.07 % Favored : 73.51 % 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: 0.17 (0.16), residues: 3144 helix: 2.06 (0.15), residues: 1362 sheet: -0.53 (0.29), residues: 354 loop : -1.75 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 694 TYR 0.020 0.001 TYR D 479 PHE 0.037 0.002 PHE B 554 TRP 0.020 0.001 TRP B 607 HIS 0.005 0.001 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00402 (19576) covalent geometry : angle 0.54262 (26984) SS BOND : bond 0.00278 ( 12) SS BOND : angle 1.81488 ( 24) hydrogen bonds : bond 0.04303 ( 1042) hydrogen bonds : angle 3.96635 ( 3057) *********************** 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 283 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 214 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 568 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7601 (tm) REVERT: A 607 MET cc_start: 0.8108 (tpp) cc_final: 0.7633 (tpp) REVERT: B 567 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7961 (mt) REVERT: B 748 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7570 (mt) REVERT: C 166 LEU cc_start: 0.8717 (tt) cc_final: 0.8295 (mp) REVERT: D 134 MET cc_start: 0.6388 (tpt) cc_final: 0.5505 (tpt) REVERT: D 554 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.7611 (m-10) REVERT: D 609 LEU cc_start: 0.8938 (mt) cc_final: 0.8688 (mt) REVERT: D 666 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8387 (pp) outliers start: 69 outliers final: 58 residues processed: 267 average time/residue: 0.0912 time to fit residues: 42.9763 Evaluate side-chains 267 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 204 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 832 SER Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 768 LYS Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 837 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 54 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 100 optimal weight: 50.0000 chunk 162 optimal weight: 40.0000 chunk 176 optimal weight: 20.0000 chunk 190 optimal weight: 40.0000 chunk 106 optimal weight: 50.0000 chunk 170 optimal weight: 0.0170 chunk 219 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 overall best weight: 0.9624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 616 ASN D 662 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.176979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.156238 restraints weight = 36919.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.155285 restraints weight = 66006.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.154023 restraints weight = 60581.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.152936 restraints weight = 54949.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.152132 restraints weight = 60657.698| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19588 Z= 0.111 Angle : 0.499 10.276 27008 Z= 0.264 Chirality : 0.042 0.182 3417 Planarity : 0.003 0.071 3552 Dihedral : 3.867 43.056 3247 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.38 % Favored : 94.56 % Rotamer: Outliers : 6.13 % Allowed : 21.19 % Favored : 72.68 % 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: 0.40 (0.16), residues: 3144 helix: 2.28 (0.15), residues: 1354 sheet: -0.38 (0.30), residues: 348 loop : -1.65 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 694 TYR 0.027 0.001 TYR A 703 PHE 0.026 0.002 PHE B 554 TRP 0.021 0.001 TRP B 607 HIS 0.003 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00255 (19576) covalent geometry : angle 0.49688 (26984) SS BOND : bond 0.00193 ( 12) SS BOND : angle 1.53831 ( 24) hydrogen bonds : bond 0.03413 ( 1042) hydrogen bonds : angle 3.71930 ( 3057) *********************** 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 279 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 213 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 568 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7546 (tm) REVERT: A 607 MET cc_start: 0.8019 (tpp) cc_final: 0.7551 (tpp) REVERT: A 709 HIS cc_start: 0.6987 (OUTLIER) cc_final: 0.6224 (p90) REVERT: B 567 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7862 (mt) REVERT: C 166 LEU cc_start: 0.8714 (tt) cc_final: 0.8271 (mp) REVERT: C 679 PHE cc_start: 0.4518 (OUTLIER) cc_final: 0.4172 (t80) REVERT: D 134 MET cc_start: 0.6326 (tpt) cc_final: 0.5468 (tpt) REVERT: D 554 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7519 (m-10) REVERT: D 631 MET cc_start: 0.5648 (tpt) cc_final: 0.5406 (tpt) REVERT: D 666 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8290 (pp) outliers start: 66 outliers final: 53 residues processed: 265 average time/residue: 0.0825 time to fit residues: 38.9883 Evaluate side-chains 263 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 204 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 832 SER Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 768 LYS Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 837 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 169 optimal weight: 0.0170 chunk 94 optimal weight: 30.0000 chunk 109 optimal weight: 10.0000 chunk 140 optimal weight: 1.9990 chunk 247 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 106 optimal weight: 20.0000 chunk 281 optimal weight: 0.9990 chunk 294 optimal weight: 1.9990 chunk 285 optimal weight: 2.9990 chunk 308 optimal weight: 0.7980 overall best weight: 1.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 616 ASN D 662 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.176328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.157309 restraints weight = 36872.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.155671 restraints weight = 57020.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.153511 restraints weight = 53013.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.152933 restraints weight = 61129.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.152095 restraints weight = 50061.454| |-----------------------------------------------------------------------------| r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19588 Z= 0.121 Angle : 0.509 10.003 27008 Z= 0.270 Chirality : 0.043 0.287 3417 Planarity : 0.003 0.069 3552 Dihedral : 3.835 42.406 3247 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.47 % Favored : 94.47 % Rotamer: Outliers : 6.04 % Allowed : 21.56 % Favored : 72.40 % 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: 0.46 (0.16), residues: 3144 helix: 2.31 (0.15), residues: 1354 sheet: -0.32 (0.30), residues: 340 loop : -1.60 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 694 TYR 0.022 0.001 TYR A 703 PHE 0.043 0.002 PHE B 554 TRP 0.019 0.001 TRP B 607 HIS 0.004 0.001 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00281 (19576) covalent geometry : angle 0.50713 (26984) SS BOND : bond 0.00191 ( 12) SS BOND : angle 1.50473 ( 24) hydrogen bonds : bond 0.03644 ( 1042) hydrogen bonds : angle 3.74120 ( 3057) ********************** 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 276 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 211 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 568 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7522 (tm) REVERT: A 607 MET cc_start: 0.8038 (tpp) cc_final: 0.7565 (tpp) REVERT: A 709 HIS cc_start: 0.6936 (OUTLIER) cc_final: 0.6312 (p90) REVERT: B 567 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7868 (mt) REVERT: B 748 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7585 (mt) REVERT: C 166 LEU cc_start: 0.8735 (tt) cc_final: 0.8313 (mp) REVERT: C 555 MET cc_start: 0.7099 (mmm) cc_final: 0.6734 (mmm) REVERT: C 679 PHE cc_start: 0.4574 (OUTLIER) cc_final: 0.4246 (t80) REVERT: D 134 MET cc_start: 0.6302 (tpt) cc_final: 0.5477 (tpt) REVERT: D 554 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7512 (m-10) REVERT: D 609 LEU cc_start: 0.8838 (mt) cc_final: 0.8630 (mt) REVERT: D 631 MET cc_start: 0.5817 (tpt) cc_final: 0.5479 (tpt) REVERT: D 666 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8341 (pp) outliers start: 65 outliers final: 54 residues processed: 261 average time/residue: 0.0823 time to fit residues: 37.9508 Evaluate side-chains 267 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 206 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain B residue 832 SER Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 768 LYS Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 837 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 303 optimal weight: 0.7980 chunk 29 optimal weight: 30.0000 chunk 211 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 274 optimal weight: 4.9990 chunk 106 optimal weight: 50.0000 chunk 132 optimal weight: 1.9990 chunk 195 optimal weight: 0.3980 chunk 300 optimal weight: 0.0010 chunk 15 optimal weight: 30.0000 chunk 33 optimal weight: 50.0000 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 662 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.178656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.158833 restraints weight = 37066.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.156465 restraints weight = 59635.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.154949 restraints weight = 57702.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.154727 restraints weight = 54428.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.153465 restraints weight = 52873.710| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19588 Z= 0.093 Angle : 0.472 9.379 27008 Z= 0.249 Chirality : 0.042 0.168 3417 Planarity : 0.003 0.072 3552 Dihedral : 3.601 41.662 3247 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.90 % Favored : 95.07 % Rotamer: Outliers : 4.65 % Allowed : 22.96 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.62 (0.16), residues: 3144 helix: 2.40 (0.15), residues: 1359 sheet: -0.26 (0.30), residues: 342 loop : -1.47 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 694 TYR 0.020 0.001 TYR A 703 PHE 0.035 0.001 PHE B 554 TRP 0.018 0.001 TRP B 607 HIS 0.002 0.001 HIS D 703 Details of bonding type rmsd covalent geometry : bond 0.00207 (19576) covalent geometry : angle 0.47077 (26984) SS BOND : bond 0.00172 ( 12) SS BOND : angle 1.30102 ( 24) hydrogen bonds : bond 0.02898 ( 1042) hydrogen bonds : angle 3.56486 ( 3057) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2499.48 seconds wall clock time: 43 minutes 51.15 seconds (2631.15 seconds total)