Starting phenix.real_space_refine on Tue Jun 17 01:36:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bib_44586/06_2025/9bib_44586.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bib_44586/06_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_44586/06_2025/9bib_44586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bib_44586/06_2025/9bib_44586.map" model { file = "/net/cci-nas-00/data/ceres_data/9bib_44586/06_2025/9bib_44586.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bib_44586/06_2025/9bib_44586.cif" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 26, 'ASP:plan': 29, 'TYR:plan': 11, 'ASN:plan1': 29, 'TRP:plan': 1, 'HIS:plan': 13, 'PHE:plan': 8, 'GLU:plan': 46, 'ARG:plan': 36} 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: {'GLN:plan1': 21, 'ASP:plan': 45, 'TYR:plan': 19, 'ASN:plan1': 24, 'TRP:plan': 7, 'HIS:plan': 9, 'PHE:plan': 18, 'GLU:plan': 45, 'ARG:plan': 19} 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: {'GLN:plan1': 26, 'ASP:plan': 29, 'TYR:plan': 11, 'ASN:plan1': 29, 'TRP:plan': 1, 'HIS:plan': 13, 'PHE:plan': 8, 'GLU:plan': 46, 'ARG:plan': 36} 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: {'GLN:plan1': 22, 'ASP:plan': 45, 'TYR:plan': 19, 'ASN:plan1': 24, 'TRP:plan': 7, 'HIS:plan': 9, 'PHE:plan': 17, 'GLU:plan': 45, 'ARG:plan': 19} 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: 13.13, per 1000 atoms: 0.68 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: 5.54 Conformation dependent library (CDL) restraints added in 3.3 seconds 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: 3.15 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: 7.54 Time building geometry restraints manager: 6.47 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 841 or resid 10 \ 01)) 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 841 or resid 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 844 or resid 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 844 or resid 10 \ 01)) } 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: 4.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 50.220 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.090 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.310 ------------------------------------------------------------------------------- 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 : 3.34 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.006 0.000 TRP C 636 HIS 0.001 0.000 HIS D 703 PHE 0.072 0.001 PHE D 614 TYR 0.004 0.000 TYR D 731 ARG 0.001 0.000 ARG D 519 Details of bonding type rmsd hydrogen bonds : bond 0.15982 ( 1042) hydrogen bonds : angle 6.02678 ( 3057) SS BOND : bond 0.00082 ( 12) SS BOND : angle 0.44953 ( 24) covalent geometry : bond 0.00445 (19576) covalent geometry : angle 0.62500 (26984) *********************** 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 : 1.994 Fit side-chains REVERT: A 807 THR cc_start: 0.8184 (t) cc_final: 0.7922 (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: 0.6717 (m-10) REVERT: C 166 LEU cc_start: 0.8403 (tt) cc_final: 0.8195 (mp) REVERT: C 584 SER cc_start: 0.5077 (t) cc_final: 0.4755 (p) REVERT: D 628 SER cc_start: 0.7181 (p) cc_final: 0.6877 (t) outliers start: 50 outliers final: 17 residues processed: 434 average time/residue: 0.2677 time to fit residues: 182.8817 Evaluate side-chains 258 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 241 time to evaluate : 2.345 ------------------------------------------------------------------------------- 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 265 optimal weight: 50.0000 chunk 237 optimal weight: 30.0000 chunk 132 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 160 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 chunk 246 optimal weight: 50.0000 chunk 95 optimal weight: 50.0000 chunk 149 optimal weight: 1.9990 chunk 183 optimal weight: 40.0000 chunk 285 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 HIS A 771 GLN 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 = 0.4259 r_free = 0.4259 target = 0.176893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.143005 restraints weight = 36315.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.139221 restraints weight = 62497.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.137497 restraints weight = 54475.312| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19588 Z= 0.166 Angle : 0.538 8.499 27008 Z= 0.294 Chirality : 0.044 0.171 3417 Planarity : 0.004 0.056 3552 Dihedral : 4.085 58.656 3263 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.39 % Favored : 95.55 % Rotamer: Outliers : 6.60 % Allowed : 15.33 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.15), residues: 3144 helix: 1.27 (0.14), residues: 1361 sheet: -0.80 (0.29), residues: 338 loop : -2.48 (0.14), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 498 HIS 0.009 0.002 HIS A 780 PHE 0.042 0.003 PHE A 533 TYR 0.023 0.002 TYR C 410 ARG 0.008 0.001 ARG D 505 Details of bonding type rmsd hydrogen bonds : bond 0.04194 ( 1042) hydrogen bonds : angle 4.22787 ( 3057) SS BOND : bond 0.00885 ( 12) SS BOND : angle 1.50547 ( 24) covalent geometry : bond 0.00386 (19576) covalent geometry : angle 0.53618 (26984) *********************** 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 326 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 255 time to evaluate : 2.035 Fit side-chains REVERT: A 348 PHE cc_start: 0.8039 (m-10) cc_final: 0.7810 (m-80) REVERT: A 544 LYS cc_start: 0.6486 (OUTLIER) cc_final: 0.6004 (mtpp) REVERT: A 607 MET cc_start: 0.8285 (tpp) cc_final: 0.7979 (tpp) REVERT: B 567 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8349 (mt) REVERT: B 607 TRP cc_start: 0.8378 (t-100) cc_final: 0.7895 (t60) REVERT: B 631 MET cc_start: 0.8354 (tpt) cc_final: 0.8094 (tpt) REVERT: C 166 LEU cc_start: 0.8864 (tt) cc_final: 0.8453 (mp) REVERT: D 476 TYR cc_start: 0.7682 (p90) cc_final: 0.7393 (p90) outliers start: 71 outliers final: 37 residues processed: 304 average time/residue: 0.2236 time to fit residues: 115.7295 Evaluate side-chains 256 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 2.252 ------------------------------------------------------------------------------- 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 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 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 824 MET Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 575 VAL 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 768 LYS Chi-restraints excluded: chain D residue 821 VAL 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 171 optimal weight: 30.0000 chunk 185 optimal weight: 40.0000 chunk 204 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 28 optimal weight: 50.0000 chunk 226 optimal weight: 0.7980 chunk 236 optimal weight: 50.0000 chunk 144 optimal weight: 2.9990 chunk 31 optimal weight: 30.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 486 HIS C 404 HIS C 705 HIS ** D 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 662 GLN ** D 703 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.170532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.140229 restraints weight = 36349.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.137423 restraints weight = 58047.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.135798 restraints weight = 57200.531| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 19588 Z= 0.230 Angle : 0.613 11.648 27008 Z= 0.337 Chirality : 0.046 0.179 3417 Planarity : 0.004 0.057 3552 Dihedral : 4.416 52.033 3248 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.25 % Favored : 94.69 % Rotamer: Outliers : 7.81 % Allowed : 15.71 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.15), residues: 3144 helix: 1.49 (0.15), residues: 1365 sheet: -0.81 (0.28), residues: 339 loop : -2.28 (0.14), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 768 HIS 0.008 0.002 HIS C 780 PHE 0.045 0.003 PHE C 533 TYR 0.029 0.002 TYR C 410 ARG 0.005 0.001 ARG B 519 Details of bonding type rmsd hydrogen bonds : bond 0.05461 ( 1042) hydrogen bonds : angle 4.41807 ( 3057) SS BOND : bond 0.00573 ( 12) SS BOND : angle 1.70573 ( 24) covalent geometry : bond 0.00554 (19576) covalent geometry : angle 0.61141 (26984) *********************** 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 315 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 231 time to evaluate : 2.281 Fit side-chains revert: symmetry clash REVERT: A 544 LYS cc_start: 0.6503 (OUTLIER) cc_final: 0.6066 (mtpp) REVERT: A 607 MET cc_start: 0.8450 (tpp) cc_final: 0.8115 (tpp) REVERT: A 693 PHE cc_start: 0.7401 (OUTLIER) cc_final: 0.7097 (t80) REVERT: B 567 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8407 (mt) REVERT: C 166 LEU cc_start: 0.8898 (tt) cc_final: 0.8411 (mp) REVERT: C 774 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8475 (mp) REVERT: D 437 GLN cc_start: 0.8011 (mt0) cc_final: 0.7594 (mp10) REVERT: D 476 TYR cc_start: 0.8047 (p90) cc_final: 0.7792 (p90) REVERT: D 554 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.7596 (m-10) outliers start: 84 outliers final: 56 residues processed: 292 average time/residue: 0.2207 time to fit residues: 111.2872 Evaluate side-chains 271 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 210 time to evaluate : 2.198 ------------------------------------------------------------------------------- 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 572 VAL Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 749 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 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 655 ILE Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 718 LEU 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 832 SER 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 575 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 687 SER Chi-restraints excluded: chain C residue 689 VAL 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 434 VAL Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 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 614 PHE Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 723 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 75 optimal weight: 0.0020 chunk 6 optimal weight: 0.9990 chunk 93 optimal weight: 50.0000 chunk 46 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 222 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 204 optimal weight: 0.0270 chunk 26 optimal weight: 20.0000 chunk 122 optimal weight: 0.9980 chunk 265 optimal weight: 50.0000 overall best weight: 1.4050 ------------------------------------------------------------------------------- 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 D 703 HIS 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 = 0.176478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.156731 restraints weight = 37041.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.155907 restraints weight = 63464.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.154087 restraints weight = 57136.314| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19588 Z= 0.132 Angle : 0.496 8.665 27008 Z= 0.269 Chirality : 0.043 0.155 3417 Planarity : 0.003 0.047 3552 Dihedral : 3.987 49.315 3248 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.74 % Favored : 95.20 % Rotamer: Outliers : 6.23 % Allowed : 18.12 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 3144 helix: 1.86 (0.15), residues: 1359 sheet: -0.79 (0.29), residues: 335 loop : -2.02 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 607 HIS 0.004 0.001 HIS A 780 PHE 0.025 0.002 PHE B 554 TYR 0.017 0.001 TYR A 681 ARG 0.005 0.001 ARG A 694 Details of bonding type rmsd hydrogen bonds : bond 0.03863 ( 1042) hydrogen bonds : angle 3.93279 ( 3057) SS BOND : bond 0.00243 ( 12) SS BOND : angle 1.40410 ( 24) covalent geometry : bond 0.00309 (19576) covalent geometry : angle 0.49416 (26984) *********************** 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 291 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 224 time to evaluate : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 568 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7622 (tm) REVERT: A 607 MET cc_start: 0.8024 (tpp) cc_final: 0.7605 (tpp) REVERT: A 709 HIS cc_start: 0.6996 (OUTLIER) cc_final: 0.5619 (p90) REVERT: B 567 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7892 (mt) REVERT: C 166 LEU cc_start: 0.8618 (tt) cc_final: 0.8333 (mp) REVERT: D 554 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7580 (m-10) outliers start: 67 outliers final: 45 residues processed: 276 average time/residue: 0.2283 time to fit residues: 110.1724 Evaluate side-chains 256 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 207 time to evaluate : 2.601 ------------------------------------------------------------------------------- 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 403 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 541 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 679 PHE 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 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 530 ILE Chi-restraints excluded: chain B residue 566 LEU 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 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 813 LEU Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 469 THR 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 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 654 MET Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 760 THR 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 183 optimal weight: 30.0000 chunk 313 optimal weight: 1.9990 chunk 254 optimal weight: 50.0000 chunk 101 optimal weight: 30.0000 chunk 234 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 310 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 102 optimal weight: 0.0070 chunk 267 optimal weight: 0.0040 chunk 294 optimal weight: 0.9980 overall best weight: 0.7412 ------------------------------------------------------------------------------- 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 = 0.4268 r_free = 0.4268 target = 0.177927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.157714 restraints weight = 37544.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.156428 restraints weight = 64915.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.154977 restraints weight = 58221.528| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19588 Z= 0.098 Angle : 0.466 8.254 27008 Z= 0.249 Chirality : 0.042 0.211 3417 Planarity : 0.003 0.064 3552 Dihedral : 3.722 47.275 3248 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.83 % Favored : 95.10 % Rotamer: Outliers : 5.67 % Allowed : 19.33 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.16), residues: 3144 helix: 2.10 (0.15), residues: 1367 sheet: -0.67 (0.29), residues: 345 loop : -1.84 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 607 HIS 0.003 0.001 HIS C 67 PHE 0.025 0.001 PHE B 554 TYR 0.015 0.001 TYR A 681 ARG 0.004 0.001 ARG A 694 Details of bonding type rmsd hydrogen bonds : bond 0.03185 ( 1042) hydrogen bonds : angle 3.69216 ( 3057) SS BOND : bond 0.00173 ( 12) SS BOND : angle 1.35388 ( 24) covalent geometry : bond 0.00216 (19576) covalent geometry : angle 0.46436 (26984) *********************** 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 290 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 229 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 568 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7581 (tm) REVERT: A 607 MET cc_start: 0.7999 (tpp) cc_final: 0.7552 (tpp) REVERT: A 693 PHE cc_start: 0.7012 (OUTLIER) cc_final: 0.6753 (t80) REVERT: A 709 HIS cc_start: 0.6953 (OUTLIER) cc_final: 0.5523 (p90) REVERT: B 748 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7487 (mt) REVERT: C 166 LEU cc_start: 0.8615 (tt) cc_final: 0.8318 (mp) REVERT: C 269 LEU cc_start: 0.6689 (tp) cc_final: 0.6466 (tp) REVERT: D 134 MET cc_start: 0.6458 (tpt) cc_final: 0.5402 (tpt) REVERT: D 554 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7525 (m-10) outliers start: 61 outliers final: 43 residues processed: 276 average time/residue: 0.2233 time to fit residues: 107.4510 Evaluate side-chains 259 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 211 time to evaluate : 2.142 ------------------------------------------------------------------------------- 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 568 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 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 566 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 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 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 726 LEU 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 628 SER Chi-restraints excluded: chain D residue 654 MET Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 760 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 33 optimal weight: 50.0000 chunk 139 optimal weight: 4.9990 chunk 277 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 214 optimal weight: 0.3980 chunk 200 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 291 optimal weight: 1.9990 chunk 28 optimal weight: 40.0000 chunk 51 optimal weight: 2.9990 chunk 281 optimal weight: 0.7980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.4261 r_free = 0.4261 target = 0.177280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.158904 restraints weight = 37341.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.156863 restraints weight = 53538.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.154386 restraints weight = 55067.559| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19588 Z= 0.108 Angle : 0.477 7.909 27008 Z= 0.254 Chirality : 0.042 0.166 3417 Planarity : 0.003 0.065 3552 Dihedral : 3.691 46.278 3247 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.80 % Favored : 95.13 % Rotamer: Outliers : 6.51 % Allowed : 20.07 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.16), residues: 3144 helix: 2.19 (0.15), residues: 1368 sheet: -0.50 (0.29), residues: 345 loop : -1.76 (0.15), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 607 HIS 0.003 0.001 HIS C 477 PHE 0.025 0.002 PHE B 554 TYR 0.014 0.001 TYR A 681 ARG 0.003 0.000 ARG A 694 Details of bonding type rmsd hydrogen bonds : bond 0.03341 ( 1042) hydrogen bonds : angle 3.68548 ( 3057) SS BOND : bond 0.00247 ( 12) SS BOND : angle 1.31117 ( 24) covalent geometry : bond 0.00248 (19576) covalent geometry : angle 0.47517 (26984) *********************** 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 291 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 221 time to evaluate : 2.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 568 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7602 (tm) REVERT: A 607 MET cc_start: 0.8052 (tpp) cc_final: 0.7588 (tpp) REVERT: A 693 PHE cc_start: 0.7043 (OUTLIER) cc_final: 0.6779 (t80) REVERT: A 709 HIS cc_start: 0.6929 (OUTLIER) cc_final: 0.5644 (p90) REVERT: B 567 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7770 (mt) REVERT: B 748 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7465 (mt) REVERT: C 166 LEU cc_start: 0.8637 (tt) cc_final: 0.8294 (mp) REVERT: D 134 MET cc_start: 0.6455 (tpt) cc_final: 0.5417 (tpt) REVERT: D 554 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7482 (m-10) outliers start: 70 outliers final: 50 residues processed: 274 average time/residue: 0.2229 time to fit residues: 107.1230 Evaluate side-chains 268 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 212 time to evaluate : 2.029 ------------------------------------------------------------------------------- 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 679 PHE Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 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 566 LEU 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 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 469 THR 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 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 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 612 LEU Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 654 MET Chi-restraints excluded: chain D residue 655 ILE 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 768 LYS 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 307 optimal weight: 0.1980 chunk 123 optimal weight: 4.9990 chunk 252 optimal weight: 0.9990 chunk 179 optimal weight: 4.9990 chunk 173 optimal weight: 30.0000 chunk 80 optimal weight: 0.0030 chunk 162 optimal weight: 40.0000 chunk 95 optimal weight: 2.9990 chunk 305 optimal weight: 2.9990 chunk 98 optimal weight: 50.0000 chunk 292 optimal weight: 0.6980 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 HIS B 616 ASN D 662 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.177795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.159239 restraints weight = 36966.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.157002 restraints weight = 52937.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.155658 restraints weight = 50320.947| |-----------------------------------------------------------------------------| r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19588 Z= 0.107 Angle : 0.476 8.616 27008 Z= 0.253 Chirality : 0.042 0.175 3417 Planarity : 0.003 0.067 3552 Dihedral : 3.650 45.414 3247 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.96 % Favored : 94.97 % Rotamer: Outliers : 5.86 % Allowed : 21.28 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.16), residues: 3144 helix: 2.25 (0.15), residues: 1369 sheet: -0.38 (0.30), residues: 329 loop : -1.68 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 607 HIS 0.003 0.001 HIS D 703 PHE 0.034 0.002 PHE D 114 TYR 0.013 0.001 TYR A 681 ARG 0.003 0.000 ARG A 694 Details of bonding type rmsd hydrogen bonds : bond 0.03323 ( 1042) hydrogen bonds : angle 3.65219 ( 3057) SS BOND : bond 0.00229 ( 12) SS BOND : angle 1.31679 ( 24) covalent geometry : bond 0.00247 (19576) covalent geometry : angle 0.47476 (26984) *********************** 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 278 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 215 time to evaluate : 2.076 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 568 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7533 (tm) REVERT: A 607 MET cc_start: 0.8053 (tpp) cc_final: 0.7596 (tpp) REVERT: A 693 PHE cc_start: 0.7086 (OUTLIER) cc_final: 0.6782 (t80) REVERT: A 709 HIS cc_start: 0.6962 (OUTLIER) cc_final: 0.5781 (p90) REVERT: B 567 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7777 (mt) REVERT: B 748 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7474 (mt) REVERT: C 166 LEU cc_start: 0.8620 (tt) cc_final: 0.8271 (mp) REVERT: D 134 MET cc_start: 0.6411 (tpt) cc_final: 0.5366 (tpt) REVERT: D 554 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7520 (m-10) outliers start: 63 outliers final: 53 residues processed: 264 average time/residue: 0.2183 time to fit residues: 101.0465 Evaluate side-chains 262 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 203 time to evaluate : 1.970 ------------------------------------------------------------------------------- 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 679 PHE Chi-restraints excluded: chain A residue 693 PHE 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 762 MET 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 566 LEU Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 616 ASN 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 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 575 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 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 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 612 LEU Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 654 MET Chi-restraints excluded: chain D residue 655 ILE 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 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 29 optimal weight: 50.0000 chunk 125 optimal weight: 0.6980 chunk 232 optimal weight: 0.0570 chunk 195 optimal weight: 0.0670 chunk 82 optimal weight: 50.0000 chunk 183 optimal weight: 50.0000 chunk 281 optimal weight: 0.0170 chunk 115 optimal weight: 0.7980 chunk 253 optimal weight: 50.0000 chunk 150 optimal weight: 0.9990 chunk 273 optimal weight: 3.9990 overall best weight: 0.3274 ------------------------------------------------------------------------------- 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 = 0.4260 r_free = 0.4260 target = 0.177082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.153608 restraints weight = 36987.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.150328 restraints weight = 52793.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.148273 restraints weight = 50587.598| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19588 Z= 0.084 Angle : 0.450 8.786 27008 Z= 0.238 Chirality : 0.041 0.177 3417 Planarity : 0.003 0.065 3552 Dihedral : 3.433 44.948 3247 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.36 % Favored : 95.61 % Rotamer: Outliers : 4.37 % Allowed : 23.14 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.16), residues: 3144 helix: 2.36 (0.15), residues: 1368 sheet: -0.14 (0.30), residues: 329 loop : -1.55 (0.16), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 607 HIS 0.003 0.001 HIS D 703 PHE 0.031 0.001 PHE B 554 TYR 0.012 0.001 TYR A 681 ARG 0.003 0.000 ARG A 694 Details of bonding type rmsd hydrogen bonds : bond 0.02574 ( 1042) hydrogen bonds : angle 3.50398 ( 3057) SS BOND : bond 0.00154 ( 12) SS BOND : angle 1.02208 ( 24) covalent geometry : bond 0.00176 (19576) covalent geometry : angle 0.44964 (26984) *********************** 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 286 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 239 time to evaluate : 2.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 568 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7623 (tm) REVERT: A 607 MET cc_start: 0.8054 (tpp) cc_final: 0.7620 (tpp) REVERT: A 693 PHE cc_start: 0.7147 (OUTLIER) cc_final: 0.6797 (t80) REVERT: B 567 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7996 (mt) REVERT: C 166 LEU cc_start: 0.8792 (tt) cc_final: 0.8285 (mp) REVERT: D 134 MET cc_start: 0.6522 (tpt) cc_final: 0.5533 (tpt) REVERT: D 554 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7512 (m-10) REVERT: D 614 PHE cc_start: 0.8013 (m-80) cc_final: 0.7797 (m-80) outliers start: 47 outliers final: 30 residues processed: 275 average time/residue: 0.2351 time to fit residues: 111.9844 Evaluate side-chains 251 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 217 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ILE 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 693 PHE Chi-restraints excluded: chain A residue 730 ILE Chi-restraints excluded: chain A residue 798 CYS 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 566 LEU 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 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 579 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL 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 628 SER Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 760 THR 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 124 optimal weight: 3.9990 chunk 76 optimal weight: 0.0050 chunk 214 optimal weight: 0.9990 chunk 17 optimal weight: 30.0000 chunk 159 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 269 optimal weight: 50.0000 chunk 237 optimal weight: 20.0000 chunk 231 optimal weight: 1.9990 chunk 304 optimal weight: 0.6980 chunk 139 optimal weight: 6.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- 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 = 0.4224 r_free = 0.4224 target = 0.173808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.148029 restraints weight = 36531.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.145070 restraints weight = 56389.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.143549 restraints weight = 50911.644| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19588 Z= 0.120 Angle : 0.495 9.506 27008 Z= 0.263 Chirality : 0.042 0.181 3417 Planarity : 0.003 0.070 3552 Dihedral : 3.616 44.399 3247 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.18 % Favored : 94.78 % Rotamer: Outliers : 4.37 % Allowed : 23.51 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.16), residues: 3144 helix: 2.42 (0.15), residues: 1363 sheet: -0.15 (0.31), residues: 316 loop : -1.53 (0.16), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 607 HIS 0.004 0.001 HIS C 477 PHE 0.033 0.002 PHE B 554 TYR 0.014 0.001 TYR B 479 ARG 0.010 0.001 ARG A 694 Details of bonding type rmsd hydrogen bonds : bond 0.03488 ( 1042) hydrogen bonds : angle 3.62697 ( 3057) SS BOND : bond 0.00221 ( 12) SS BOND : angle 1.48290 ( 24) covalent geometry : bond 0.00279 (19576) covalent geometry : angle 0.49364 (26984) *********************** 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 263 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 216 time to evaluate : 3.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 568 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7700 (tm) REVERT: A 607 MET cc_start: 0.8199 (tpp) cc_final: 0.7757 (tpp) REVERT: A 693 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.6893 (t80) REVERT: A 709 HIS cc_start: 0.6866 (OUTLIER) cc_final: 0.5787 (p90) REVERT: B 567 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8064 (mt) REVERT: C 166 LEU cc_start: 0.8805 (tt) cc_final: 0.8322 (mp) REVERT: D 134 MET cc_start: 0.6526 (tpt) cc_final: 0.5495 (tpt) REVERT: D 554 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7532 (m-10) REVERT: D 818 MET cc_start: 0.8105 (mmt) cc_final: 0.7433 (mmt) outliers start: 47 outliers final: 35 residues processed: 255 average time/residue: 0.3317 time to fit residues: 149.3864 Evaluate side-chains 252 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 212 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 693 PHE 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 774 LEU Chi-restraints excluded: chain A residue 798 CYS 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 566 LEU 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 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 575 VAL Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 643 ILE 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 436 CYS Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 628 SER Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 760 THR 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 43 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 112 optimal weight: 50.0000 chunk 60 optimal weight: 0.7980 chunk 31 optimal weight: 40.0000 chunk 134 optimal weight: 0.5980 chunk 216 optimal weight: 0.5980 chunk 189 optimal weight: 20.0000 chunk 114 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.4219 r_free = 0.4219 target = 0.173387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.147622 restraints weight = 36780.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.146199 restraints weight = 57276.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.144212 restraints weight = 52172.670| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19588 Z= 0.121 Angle : 0.494 10.048 27008 Z= 0.264 Chirality : 0.043 0.182 3417 Planarity : 0.003 0.070 3552 Dihedral : 3.674 41.045 3247 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.18 % Favored : 94.78 % Rotamer: Outliers : 4.46 % Allowed : 23.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.16), residues: 3144 helix: 2.37 (0.15), residues: 1361 sheet: -0.11 (0.31), residues: 334 loop : -1.48 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 607 HIS 0.003 0.001 HIS C 477 PHE 0.032 0.002 PHE B 554 TYR 0.021 0.001 TYR C 703 ARG 0.010 0.001 ARG A 694 Details of bonding type rmsd hydrogen bonds : bond 0.03493 ( 1042) hydrogen bonds : angle 3.64899 ( 3057) SS BOND : bond 0.00190 ( 12) SS BOND : angle 1.47811 ( 24) covalent geometry : bond 0.00283 (19576) covalent geometry : angle 0.49211 (26984) ********************** 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 265 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 217 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 568 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7593 (tm) REVERT: A 607 MET cc_start: 0.8165 (tpp) cc_final: 0.7699 (tpp) REVERT: A 693 PHE cc_start: 0.7356 (OUTLIER) cc_final: 0.6989 (t80) REVERT: A 709 HIS cc_start: 0.6910 (OUTLIER) cc_final: 0.5966 (p90) REVERT: B 567 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8089 (mt) REVERT: C 166 LEU cc_start: 0.8824 (tt) cc_final: 0.8314 (mp) REVERT: C 679 PHE cc_start: 0.4710 (OUTLIER) cc_final: 0.4464 (t80) REVERT: D 134 MET cc_start: 0.6433 (tpt) cc_final: 0.5495 (tpt) REVERT: D 554 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7604 (m-10) REVERT: D 818 MET cc_start: 0.8156 (mmt) cc_final: 0.7322 (mmt) outliers start: 48 outliers final: 38 residues processed: 256 average time/residue: 0.2629 time to fit residues: 118.2012 Evaluate side-chains 259 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 215 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 693 PHE 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 798 CYS 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 530 ILE Chi-restraints excluded: chain B residue 566 LEU 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 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 476 VAL Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 643 ILE 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 436 CYS 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 628 SER Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 760 THR 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 175 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 280 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 163 optimal weight: 20.0000 chunk 264 optimal weight: 0.9980 chunk 300 optimal weight: 0.8980 chunk 169 optimal weight: 0.0870 chunk 199 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 chunk 244 optimal weight: 0.0470 overall best weight: 0.5456 ------------------------------------------------------------------------------- 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 = 0.4254 r_free = 0.4254 target = 0.176517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.153290 restraints weight = 37846.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.150706 restraints weight = 64295.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.149436 restraints weight = 59620.451| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19588 Z= 0.091 Angle : 0.469 9.662 27008 Z= 0.248 Chirality : 0.042 0.185 3417 Planarity : 0.003 0.072 3552 Dihedral : 3.487 40.626 3247 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.71 % Favored : 95.26 % Rotamer: Outliers : 4.09 % Allowed : 23.70 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.16), residues: 3144 helix: 2.46 (0.15), residues: 1368 sheet: -0.03 (0.30), residues: 351 loop : -1.40 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 607 HIS 0.002 0.001 HIS D 703 PHE 0.039 0.001 PHE B 554 TYR 0.016 0.001 TYR C 703 ARG 0.009 0.000 ARG A 694 Details of bonding type rmsd hydrogen bonds : bond 0.02819 ( 1042) hydrogen bonds : angle 3.50708 ( 3057) SS BOND : bond 0.00158 ( 12) SS BOND : angle 1.17078 ( 24) covalent geometry : bond 0.00201 (19576) covalent geometry : angle 0.46802 (26984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6948.78 seconds wall clock time: 124 minutes 34.34 seconds (7474.34 seconds total)